HEADER ELECTRON TRANSPORT 12-JUN-11 3ZQV TITLE RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS AT TITLE 2 0.84 A RESOLUTION: NON-RESTRAINED REFINEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACHROMOBACTER XYLOSOXIDANS; SOURCE 3 ORGANISM_TAXID: 85698; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PEC86 KEYWDS ELECTRON TRANSPORT, HAEMOPROTEIN, 4-HELIX BUNDLE EXPDTA X-RAY DIFFRACTION AUTHOR S.V.ANTONYUK,R.R.EADY,S.S.HASNAIN REVDAT 2 11-MAR-20 3ZQV 1 SEQRES LINK ATOM REVDAT 1 05-OCT-11 3ZQV 0 JRNL AUTH S.V.ANTONYUK,N.RUSTAGE,C.A.PETERSEN,J.L.ARNST,D.J.HEYES, JRNL AUTH 2 R.SHARMA,N.G.BERRY,N.S.SCRUTTON,R.R.EADY,C.R.ANDREW, JRNL AUTH 3 S.S.HASNAIN JRNL TITL CARBON MONOXIDE POISONING IS PREVENTED BY THE ENERGY COSTS JRNL TITL 2 OF CONFORMATIONAL CHANGES IN GAS- BINDING HAEMPROTEINS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 15780 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 21900609 JRNL DOI 10.1073/PNAS.1109051108 REMARK 2 REMARK 2 RESOLUTION. 0.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.108 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 128681 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.096 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 102205 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 952 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 381 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.043 REMARK 3 ANGLE DISTANCES (A) : 2.764 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3ZQV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-JUN-11. REMARK 100 THE DEPOSITION ID IS D_1290048679. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.79 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 128930 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.840 REMARK 200 RESOLUTION RANGE LOW (A) : 19.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.78000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.120 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULPHATE, PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 120.79333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 60.39667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 90.59500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 30.19833 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 150.99167 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 120.79333 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 60.39667 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 30.19833 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 90.59500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 150.99167 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -93.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.500000 -0.866025 0.000000 26.73500 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 46.30638 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 30.19833 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2063 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 127 CA C O CB CG CD CE REMARK 470 LYS A 127 NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 2092 O HOH A 2095 1.38 REMARK 500 HZ3 LYS A 31 O HOH A 2148 1.53 REMARK 500 OE2 GLU A 46 O HOH A 2217 1.95 REMARK 500 O HOH A 2224 O HOH A 2227 1.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 4 CB LYS A 4 CG 0.362 REMARK 500 LYS A 4 CD LYS A 4 CE 0.251 REMARK 500 LYS A 4 CE LYS A 4 NZ 0.515 REMARK 500 PRO A 5 CG PRO A 5 CD -0.284 REMARK 500 GLU A 6 CG GLU A 6 CD -0.101 REMARK 500 GLU A 6 CD GLU A 6 OE1 0.072 REMARK 500 LYS A 10 CD LYS A 10 CE -0.333 REMARK 500 SER A 14 CB SER A 14 OG 0.130 REMARK 500 ALA A 20 C ALA A 20 O 0.348 REMARK 500 VAL A 30 CB VAL A 30 CG2 -0.265 REMARK 500 VAL A 30 CB VAL A 30 CG2 0.153 REMARK 500 GLN A 33 CG GLN A 33 CD 0.163 REMARK 500 GLN A 33 CD GLN A 33 OE1 -0.212 REMARK 500 GLN A 33 CD GLN A 33 NE2 0.211 REMARK 500 ASP A 37 CB ASP A 37 CG 0.163 REMARK 500 GLN A 40 CD GLN A 40 OE1 0.166 REMARK 500 GLU A 46 CG GLU A 46 CD -0.114 REMARK 500 GLU A 46 CG GLU A 46 CD 0.164 REMARK 500 GLU A 46 CD GLU A 46 OE1 0.195 REMARK 500 GLU A 46 CD GLU A 46 OE1 -0.077 REMARK 500 GLU A 46 CD GLU A 46 OE2 -0.094 REMARK 500 GLU A 46 CD GLU A 46 OE2 0.066 REMARK 500 LYS A 49 CD LYS A 49 CE 0.275 REMARK 500 LYS A 49 CE LYS A 49 NZ 0.501 REMARK 500 SER A 52 CB SER A 52 OG -0.086 REMARK 500 PHE A 59 C GLY A 60 N 0.157 REMARK 500 GLY A 60 CA GLY A 60 C -0.164 REMARK 500 GLY A 60 C GLY A 60 O -0.134 REMARK 500 GLY A 60 C PRO A 61 N -0.208 REMARK 500 PRO A 61 N PRO A 61 CA 0.225 REMARK 500 PRO A 61 CB PRO A 61 CG -0.350 REMARK 500 PRO A 61 CG PRO A 61 CD 0.255 REMARK 500 PRO A 61 CD PRO A 61 N 0.121 REMARK 500 PRO A 61 CA PRO A 61 C -0.126 REMARK 500 PRO A 61 C PRO A 61 O -0.249 REMARK 500 GLY A 62 N GLY A 62 CA 0.150 REMARK 500 ARG A 69 CG ARG A 69 CD 0.435 REMARK 500 ARG A 69 CD ARG A 69 NE -0.203 REMARK 500 ARG A 69 NE ARG A 69 CZ 0.243 REMARK 500 ARG A 69 CZ ARG A 69 NH2 0.142 REMARK 500 TRP A 73 C SER A 74 N 0.171 REMARK 500 SER A 74 N SER A 74 CA 0.121 REMARK 500 SER A 74 CA SER A 74 CB 0.178 REMARK 500 SER A 74 C SER A 74 O 0.181 REMARK 500 ASP A 75 CA ASP A 75 CB -0.226 REMARK 500 ASP A 75 CB ASP A 75 CG 0.536 REMARK 500 ASP A 75 CG ASP A 75 OD1 0.180 REMARK 500 ASP A 75 CG ASP A 75 OD2 -0.141 REMARK 500 ASP A 75 CA ASP A 75 C -0.182 REMARK 500 ALA A 76 N ALA A 76 CA 0.120 REMARK 500 REMARK 500 THIS ENTRY HAS 69 BOND DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LYS A 4 CB - CG - CD ANGL. DEV. = -17.7 DEGREES REMARK 500 LYS A 4 CG - CD - CE ANGL. DEV. = -27.2 DEGREES REMARK 500 LYS A 4 CD - CE - NZ ANGL. DEV. = -30.0 DEGREES REMARK 500 LYS A 10 CD - CE - NZ ANGL. DEV. = 42.1 DEGREES REMARK 500 ALA A 20 O - C - N ANGL. DEV. = -24.2 DEGREES REMARK 500 VAL A 30 CA - CB - CG2 ANGL. DEV. = 15.4 DEGREES REMARK 500 ASP A 37 CB - CG - OD1 ANGL. DEV. = 9.8 DEGREES REMARK 500 GLU A 46 CG - CD - OE2 ANGL. DEV. = -14.6 DEGREES REMARK 500 LYS A 49 CD - CE - NZ ANGL. DEV. = -24.8 DEGREES REMARK 500 PHE A 59 CA - C - N ANGL. DEV. = 17.2 DEGREES REMARK 500 PHE A 59 O - C - N ANGL. DEV. = -17.1 DEGREES REMARK 500 GLY A 60 C - N - CA ANGL. DEV. = 13.6 DEGREES REMARK 500 PRO A 61 CB - CA - C ANGL. DEV. = 15.8 DEGREES REMARK 500 PRO A 61 N - CA - CB ANGL. DEV. = -14.3 DEGREES REMARK 500 PRO A 61 N - CD - CG ANGL. DEV. = -13.3 DEGREES REMARK 500 PRO A 61 CA - C - O ANGL. DEV. = 15.9 DEGREES REMARK 500 PRO A 61 CA - C - N ANGL. DEV. = -21.7 DEGREES REMARK 500 GLY A 62 C - N - CA ANGL. DEV. = -14.1 DEGREES REMARK 500 ARG A 69 CD - NE - CZ ANGL. DEV. = 16.8 DEGREES REMARK 500 ARG A 69 NH1 - CZ - NH2 ANGL. DEV. = -7.8 DEGREES REMARK 500 ARG A 69 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 69 NE - CZ - NH2 ANGL. DEV. = -13.3 DEGREES REMARK 500 TRP A 73 O - C - N ANGL. DEV. = 15.3 DEGREES REMARK 500 SER A 74 C - N - CA ANGL. DEV. = -25.9 DEGREES REMARK 500 SER A 74 N - CA - CB ANGL. DEV. = -18.3 DEGREES REMARK 500 SER A 74 O - C - N ANGL. DEV. = -13.7 DEGREES REMARK 500 ASP A 75 CB - CA - C ANGL. DEV. = -30.3 DEGREES REMARK 500 ASP A 75 OD1 - CG - OD2 ANGL. DEV. = 14.9 DEGREES REMARK 500 ASP A 75 CB - CG - OD1 ANGL. DEV. = -16.0 DEGREES REMARK 500 ASP A 75 CA - C - O ANGL. DEV. = 36.3 DEGREES REMARK 500 ASP A 75 CA - C - N ANGL. DEV. = -28.1 DEGREES REMARK 500 ASP A 75 O - C - N ANGL. DEV. = -17.5 DEGREES REMARK 500 ALA A 76 CB - CA - C ANGL. DEV. = -18.4 DEGREES REMARK 500 ALA A 76 N - CA - CB ANGL. DEV. = 15.4 DEGREES REMARK 500 ALA A 76 CA - C - N ANGL. DEV. = 13.7 DEGREES REMARK 500 ALA A 76 O - C - N ANGL. DEV. = -11.4 DEGREES REMARK 500 LYS A 82 CA - CB - CG ANGL. DEV. = 25.8 DEGREES REMARK 500 ASN A 89 CB - CG - OD1 ANGL. DEV. = -18.4 DEGREES REMARK 500 ALA A 99 CA - C - N ANGL. DEV. = 15.3 DEGREES REMARK 500 ALA A 99 O - C - N ANGL. DEV. = -15.9 DEGREES REMARK 500 LEU A 102 CB - CG - CD2 ANGL. DEV. = 17.8 DEGREES REMARK 500 LEU A 102 N - CA - C ANGL. DEV. = 16.6 DEGREES REMARK 500 ASP A 103 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG A 106 CD - NE - CZ ANGL. DEV. = 36.2 DEGREES REMARK 500 ARG A 106 NH1 - CZ - NH2 ANGL. DEV. = -19.0 DEGREES REMARK 500 ARG A 106 NE - CZ - NH1 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG A 106 NE - CZ - NH1 ANGL. DEV. = -25.8 DEGREES REMARK 500 ARG A 106 NE - CZ - NH2 ANGL. DEV. = 41.4 DEGREES REMARK 500 CYS A 116 CA - CB - SG ANGL. DEV. = 7.6 DEGREES REMARK 500 LYS A 117 N - CA - CB ANGL. DEV. = -10.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 51 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE A 59 40.78 -109.68 REMARK 500 PRO A 61 131.67 -37.59 REMARK 500 THR A 63 30.68 -97.23 REMARK 500 ASP A 75 84.02 -168.75 REMARK 500 ALA A 76 -78.50 -70.98 REMARK 500 ALA A 77 -40.04 -28.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 74 ASP A 75 145.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 GLN A 33 0.09 SIDE CHAIN REMARK 500 ARG A 69 0.17 SIDE CHAIN REMARK 500 ASP A 75 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ALA A 20 25.72 REMARK 500 GLY A 60 15.27 REMARK 500 SER A 74 -23.50 REMARK 500 ASP A 75 -11.02 REMARK 500 ALA A 76 18.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2037 DISTANCE = 6.81 ANGSTROMS REMARK 525 HOH A2077 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A2085 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH A2086 DISTANCE = 6.14 ANGSTROMS REMARK 525 HOH A2134 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH A2178 DISTANCE = 6.14 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 128 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 120 NE2 REMARK 620 2 HEC A 128 NA 101.1 REMARK 620 3 HEC A 128 NB 95.1 89.5 REMARK 620 4 HEC A 128 NC 96.2 162.8 89.1 REMARK 620 5 HEC A 128 ND 97.8 88.3 167.0 89.2 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A 128 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 129 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 130 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2YL3 RELATED DB: PDB REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: CARBON MONOOXIDE REMARK 900 BOUND L16G VARIANT AT 1.04 A RESOLUTION REMARK 900 RELATED ID: 2XM0 RELATED DB: PDB REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124K REMARK 900 VARIANT REMARK 900 RELATED ID: 2XLH RELATED DB: PDB REMARK 900 REDUCED STRUCTURE OF R124A MUTANT OF CYTOCHROME C' FROM ALCALIGENES REMARK 900 XYLOSOXIDANS REMARK 900 RELATED ID: 1CGO RELATED DB: PDB REMARK 900 CYTOCHROME C' REMARK 900 RELATED ID: 2YKZ RELATED DB: PDB REMARK 900 RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS REMARK 900 AT 0.84 A RESOLUTION: RESTRAINED REFINEMENT REMARK 900 RELATED ID: 2YLI RELATED DB: PDB REMARK 900 RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS REMARK 900 IN ITS FERROUS FORM AT 1.45 A REMARK 900 RELATED ID: 2XM4 RELATED DB: PDB REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124E REMARK 900 VARIANT REMARK 900 RELATED ID: 1E86 RELATED DB: PDB REMARK 900 CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS - REDUCED STRUCTURE REMARK 900 WITH CO BOUND TO DISTAL SIDE OF HEME REMARK 900 RELATED ID: 2XL6 RELATED DB: PDB REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124A REMARK 900 VARIANT WITH BOUND NO REMARK 900 RELATED ID: 2YL0 RELATED DB: PDB REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: AS ISOLATED L16A REMARK 900 VARIANT AT 0.95 A RESOLUTION REMARK 900 RELATED ID: 2YLG RELATED DB: PDB REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: ASCORBATE AND REMARK 900 CARBON MONOOXIDE BOUND L16A VARIANT AT 1 .05 A RESOLUTION REMARK 900 RELATED ID: 1E85 RELATED DB: PDB REMARK 900 CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS - REDUCED STRUCTURE REMARK 900 WITH NO BOUND TO PROXIMAL SIDE OF HEME REMARK 900 RELATED ID: 1CGN RELATED DB: PDB REMARK 900 CYTOCHROME C' REMARK 900 RELATED ID: 2XLM RELATED DB: PDB REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS REMARK 900 RECOMBINANT NATIVE WITH BOUND NO REMARK 900 RELATED ID: 2YL1 RELATED DB: PDB REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: CARBON MONOOXIDE REMARK 900 BOUND L16A VARIANT AT 1.03 A RESOLUTION - RESTRAINT REFINEMENT REMARK 900 RELATED ID: 2YLD RELATED DB: PDB REMARK 900 RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: REMARK 900 CARBON MONOOXIDE BOUND AT 1.25 A REMARK 900 RELATED ID: 2XLD RELATED DB: PDB REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124Q REMARK 900 VARIANT REMARK 900 RELATED ID: 2XLE RELATED DB: PDB REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124K REMARK 900 VARIANT WITH BOUND NO REMARK 900 RELATED ID: 2YL7 RELATED DB: PDB REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: AS ISOLATED L16G REMARK 900 VARIANT AT 0.9 A RESOLUTION - RESTRAINT REFINEMENT REMARK 900 RELATED ID: 1E83 RELATED DB: PDB REMARK 900 CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS - OXIDIZED STRUCTURE REMARK 900 RELATED ID: 2XLW RELATED DB: PDB REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124Q REMARK 900 VARIANT WITH BOUND NO REMARK 900 RELATED ID: 2XL8 RELATED DB: PDB REMARK 900 REDUCED STRUCTURE OF R124F MUTANT OF CYTOCHROME C' FROM ALCALIGENES REMARK 900 XYLOSOXIDANS REMARK 900 RELATED ID: 1E84 RELATED DB: PDB REMARK 900 CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS - REDUCED STRUCTURE REMARK 900 RELATED ID: 2XLV RELATED DB: PDB REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124F REMARK 900 VARIANT WITH BOUND NO REMARK 900 RELATED ID: 2XLO RELATED DB: PDB REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124E REMARK 900 VARIANT WITH BOUND NO REMARK 900 RELATED ID: 3ZQY RELATED DB: PDB REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: CARBON MONOOXIDE REMARK 900 BOUND L16A VARIANT AT 1.03 A RESOLUTION- NON-RESTRAINT REFINEMENT DBREF 3ZQV A 1 127 UNP P00138 CYCP_ALCXX 1 127 SEQADV 3ZQV VAL A 39 UNP P00138 ALA 39 CONFLICT SEQRES 1 A 127 PCA PHE ALA LYS PRO GLU ASP ALA VAL LYS TYR ARG GLN SEQRES 2 A 127 SER ALA LEU THR LEU MET ALA SER HIS PHE GLY ARG MET SEQRES 3 A 127 THR PRO VAL VAL LYS GLY GLN ALA PRO TYR ASP ALA VAL SEQRES 4 A 127 GLN ILE LYS ALA ASN VAL GLU VAL LEU LYS THR LEU SER SEQRES 5 A 127 ALA LEU PRO TRP ALA ALA PHE GLY PRO GLY THR GLU GLY SEQRES 6 A 127 GLY ASP ALA ARG PRO GLU ILE TRP SER ASP ALA ALA SER SEQRES 7 A 127 PHE LYS GLN LYS GLN GLN ALA PHE GLN ASP ASN ILE VAL SEQRES 8 A 127 LYS LEU SER ALA ALA ALA ASP ALA GLY ASP LEU ASP LYS SEQRES 9 A 127 LEU ARG ALA ALA PHE GLY ASP VAL GLY ALA SER CYS LYS SEQRES 10 A 127 ALA CYS HIS ASP ALA TYR ARG LYS LYS LYS MODRES 3ZQV PCA A 1 GLU PYROGLUTAMIC ACID HET PCA A 1 8 HET HEC A 128 43 HET SO4 A 129 5 HET SO4 A 130 5 HETNAM PCA PYROGLUTAMIC ACID HETNAM HEC HEME C HETNAM SO4 SULFATE ION FORMUL 1 PCA C5 H7 N O3 FORMUL 2 HEC C34 H34 FE N4 O4 FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *381(H2 O) HELIX 1 1 LYS A 4 ARG A 25 1 22 HELIX 2 2 MET A 26 LYS A 31 1 6 HELIX 3 3 ASP A 37 ALA A 53 1 17 HELIX 4 4 PRO A 55 PHE A 59 5 5 HELIX 5 5 PRO A 70 ASP A 75 1 6 HELIX 6 6 ASP A 75 GLY A 100 1 26 HELIX 7 7 ASP A 101 ARG A 124 1 24 LINK C PCA A 1 N PHE A 2 1555 1555 1.33 LINK SG CYS A 116 CAB HEC A 128 1555 1555 1.85 LINK SG CYS A 119 CAC HEC A 128 1555 1555 1.82 LINK NE2 HIS A 120 FE HEC A 128 1555 1555 2.09 SITE 1 AC1 22 ARG A 12 GLN A 13 LEU A 16 THR A 17 SITE 2 AC1 22 MET A 19 ALA A 20 TRP A 56 PHE A 59 SITE 3 AC1 22 GLY A 65 ASP A 67 GLN A 83 PHE A 86 SITE 4 AC1 22 CYS A 116 CYS A 119 HIS A 120 TYR A 123 SITE 5 AC1 22 ARG A 124 SO4 A 129 HOH A2091 HOH A2373 SITE 6 AC1 22 HOH A2374 HOH A2375 SITE 1 AC2 6 ARG A 124 HEC A 128 HOH A2364 HOH A2365 SITE 2 AC2 6 HOH A2377 HOH A2378 SITE 1 AC3 9 SER A 74 ASP A 75 ALA A 76 ALA A 77 SITE 2 AC3 9 LYS A 104 HOH A2272 HOH A2379 HOH A2380 SITE 3 AC3 9 HOH A2381 CRYST1 53.470 53.470 181.190 90.00 90.00 120.00 P 65 2 2 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.018702 0.010798 0.000000 0.00000 SCALE2 0.000000 0.021595 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005519 0.00000