HEADER TRANSFERASE 17-NOV-92 1PDA TITLE STRUCTURE OF PORPHOBILINOGEN DEAMINASE REVEALS A FLEXIBLE MULTIDOMAIN TITLE 2 POLYMERASE WITH A SINGLE CATALYTIC SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PORPHOBILINOGEN DEAMINASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.5.1.61; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562 KEYWDS PORPHYRIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.V.LOUIE,P.D.BROWNLIE,R.LAMBERT,J.B.COOPER,T.L.BLUNDELL,S.P.WOOD, AUTHOR 2 M.J.WARREN,S.C.WOODCOCK,P.M.JORDAN REVDAT 7 14-AUG-19 1PDA 1 REMARK REVDAT 6 17-JUL-19 1PDA 1 REMARK LINK REVDAT 5 29-NOV-17 1PDA 1 HELIX REVDAT 4 18-SEP-13 1PDA 1 HETNAM VERSN REVDAT 3 27-APR-11 1PDA 1 HEADER COMPND REVDAT 2 24-FEB-09 1PDA 1 VERSN REVDAT 1 31-OCT-93 1PDA 0 JRNL AUTH G.V.LOUIE,P.D.BROWNLIE,R.LAMBERT,J.B.COOPER,T.L.BLUNDELL, JRNL AUTH 2 S.P.WOOD,M.J.WARREN,S.C.WOODCOCK,P.M.JORDAN JRNL TITL STRUCTURE OF PORPHOBILINOGEN DEAMINASE REVEALS A FLEXIBLE JRNL TITL 2 MULTIDOMAIN POLYMERASE WITH A SINGLE CATALYTIC SITE. JRNL REF NATURE V. 359 33 1992 JRNL REFN ISSN 0028-0836 JRNL PMID 1522882 JRNL DOI 10.1038/359033A0 REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL 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) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2244 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 249 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.870 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.610 ; 1.800 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.530 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.300 ; 2.500 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1PDA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000175612. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 44.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.95000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.95000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 LEU A 2 REMARK 465 LEU A 49 REMARK 465 ASP A 50 REMARK 465 THR A 51 REMARK 465 PRO A 52 REMARK 465 LEU A 53 REMARK 465 ALA A 54 REMARK 465 LYS A 55 REMARK 465 VAL A 56 REMARK 465 GLY A 57 REMARK 465 ASN A 308 REMARK 465 GLY A 309 REMARK 465 ASP A 310 REMARK 465 ALA A 311 REMARK 465 PRO A 312 REMARK 465 ALA A 313 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 ARG A 44 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 59 CG CD CE NZ REMARK 470 LEU A 61 CG CD1 CD2 REMARK 470 ALA A 241 CB REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 413 O HOH A 506 3546 2.18 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 ARG A 11 NE - CZ - NH2 ANGL. DEV. = -8.0 DEGREES REMARK 500 MET A 28 CA - CB - CG ANGL. DEV. = -14.7 DEGREES REMARK 500 MET A 28 CG - SD - CE ANGL. DEV. = -14.1 DEGREES REMARK 500 LYS A 59 N - CA - CB ANGL. DEV. = 12.1 DEGREES REMARK 500 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 7.5 DEGREES REMARK 500 ARG A 74 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ASP A 84 CB - CG - OD1 ANGL. DEV. = 10.2 DEGREES REMARK 500 ASP A 84 CB - CG - OD2 ANGL. DEV. = -7.4 DEGREES REMARK 500 GLU A 88 OE1 - CD - OE2 ANGL. DEV. = 15.4 DEGREES REMARK 500 GLU A 88 CG - CD - OE1 ANGL. DEV. = -13.4 DEGREES REMARK 500 GLN A 91 N - CA - CB ANGL. DEV. = -11.3 DEGREES REMARK 500 ASP A 103 CB - CG - OD1 ANGL. DEV. = 7.3 DEGREES REMARK 500 ASP A 103 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG A 105 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 ASP A 106 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ASP A 106 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 TYR A 113 CB - CG - CD1 ANGL. DEV. = -3.6 DEGREES REMARK 500 ASP A 114 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG A 131 NE - CZ - NH1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 132 NE - CZ - NH1 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG A 139 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 149 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 155 NE - CZ - NH2 ANGL. DEV. = 5.1 DEGREES REMARK 500 ASP A 160 CB - CG - OD1 ANGL. DEV. = 7.9 DEGREES REMARK 500 ASP A 160 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 TYR A 164 CB - CG - CD1 ANGL. DEV. = 6.9 DEGREES REMARK 500 TYR A 164 CG - CD1 - CE1 ANGL. DEV. = 7.8 DEGREES REMARK 500 TYR A 164 CZ - CE2 - CD2 ANGL. DEV. = 7.5 DEGREES REMARK 500 ARG A 176 NE - CZ - NH2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG A 182 NE - CZ - NH1 ANGL. DEV. = 7.8 DEGREES REMARK 500 ARG A 182 NE - CZ - NH2 ANGL. DEV. = -9.8 DEGREES REMARK 500 ARG A 184 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 206 NE - CZ - NH1 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG A 211 CD - NE - CZ ANGL. DEV. = 8.9 DEGREES REMARK 500 ARG A 213 NE - CZ - NH1 ANGL. DEV. = -3.0 DEGREES REMARK 500 GLU A 223 OE1 - CD - OE2 ANGL. DEV. = 8.0 DEGREES REMARK 500 ARG A 232 CD - NE - CZ ANGL. DEV. = 9.7 DEGREES REMARK 500 MET A 234 CA - CB - CG ANGL. DEV. = 10.4 DEGREES REMARK 500 ASN A 235 OD1 - CG - ND2 ANGL. DEV. = 16.5 DEGREES REMARK 500 ARG A 237 NH1 - CZ - NH2 ANGL. DEV. = -6.9 DEGREES REMARK 500 ARG A 237 NE - CZ - NH1 ANGL. DEV. = 8.2 DEGREES REMARK 500 GLU A 251 OE1 - CD - OE2 ANGL. DEV. = 11.0 DEGREES REMARK 500 ARG A 276 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 276 NE - CZ - NH2 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 277 CD - NE - CZ ANGL. DEV. = -8.4 DEGREES REMARK 500 ARG A 277 NE - CZ - NH1 ANGL. DEV. = -6.8 DEGREES REMARK 500 ARG A 277 NE - CZ - NH2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASN A 297 OD1 - CG - ND2 ANGL. DEV. = 15.4 DEGREES REMARK 500 ASN A 297 CB - CG - OD1 ANGL. DEV. = -13.9 DEGREES REMARK 500 GLU A 305 CA - CB - CG ANGL. DEV. = 13.8 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 LYS A 59 -160.46 -103.63 REMARK 500 THR A 127 139.69 -172.11 REMARK 500 ALA A 241 -176.21 170.93 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 PRO A 245 10.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: DPM REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DPM A 314 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 315 DBREF 1PDA A 1 313 UNP P06983 HEM3_ECOLI 1 313 SEQADV 1PDA ALA A 241 UNP P06983 GLY 241 CONFLICT SEQADV 1PDA GLY A 261 UNP P06983 ALA 261 CONFLICT SEQRES 1 A 313 MET LEU ASP ASN VAL LEU ARG ILE ALA THR ARG GLN SER SEQRES 2 A 313 PRO LEU ALA LEU TRP GLN ALA HIS TYR VAL LYS ASP LYS SEQRES 3 A 313 LEU MET ALA SER HIS PRO GLY LEU VAL VAL GLU LEU VAL SEQRES 4 A 313 PRO MET VAL THR ARG GLY ASP VAL ILE LEU ASP THR PRO SEQRES 5 A 313 LEU ALA LYS VAL GLY GLY LYS GLY LEU PHE VAL LYS GLU SEQRES 6 A 313 LEU GLU VAL ALA LEU LEU GLU ASN ARG ALA ASP ILE ALA SEQRES 7 A 313 VAL HIS SER MET LYS ASP VAL PRO VAL GLU PHE PRO GLN SEQRES 8 A 313 GLY LEU GLY LEU VAL THR ILE CYS GLU ARG GLU ASP PRO SEQRES 9 A 313 ARG ASP ALA PHE VAL SER ASN ASN TYR ASP SER LEU ASP SEQRES 10 A 313 ALA LEU PRO ALA GLY SER ILE VAL GLY THR SER SER LEU SEQRES 11 A 313 ARG ARG GLN CYS GLN LEU ALA GLU ARG ARG PRO ASP LEU SEQRES 12 A 313 ILE ILE ARG SER LEU ARG GLY ASN VAL GLY THR ARG LEU SEQRES 13 A 313 SER LYS LEU ASP ASN GLY GLU TYR ASP ALA ILE ILE LEU SEQRES 14 A 313 ALA VAL ALA GLY LEU LYS ARG LEU GLY LEU GLU SER ARG SEQRES 15 A 313 ILE ARG ALA ALA LEU PRO PRO GLU ILE SER LEU PRO ALA SEQRES 16 A 313 VAL GLY GLN GLY ALA VAL GLY ILE GLU CYS ARG LEU ASP SEQRES 17 A 313 ASP SER ARG THR ARG GLU LEU LEU ALA ALA LEU ASN HIS SEQRES 18 A 313 HIS GLU THR ALA LEU ARG VAL THR ALA GLU ARG ALA MET SEQRES 19 A 313 ASN THR ARG LEU GLU GLY ALA CYS GLN VAL PRO ILE GLY SEQRES 20 A 313 SER TYR ALA GLU LEU ILE ASP GLY GLU ILE TRP LEU ARG SEQRES 21 A 313 GLY LEU VAL GLY ALA PRO ASP GLY SER GLN ILE ILE ARG SEQRES 22 A 313 GLY GLU ARG ARG GLY ALA PRO GLN ASP ALA GLU GLN MET SEQRES 23 A 313 GLY ILE SER LEU ALA GLU GLU LEU LEU ASN ASN GLY ALA SEQRES 24 A 313 ARG GLU ILE LEU ALA GLU VAL TYR ASN GLY ASP ALA PRO SEQRES 25 A 313 ALA HET DPM A 314 30 HET ACY A 315 4 HETNAM DPM 3-[5-{[3-(2-CARBOXYETHYL)-4-(CARBOXYMETHYL)-5-METHYL- HETNAM 2 DPM 1H-PYRROL-2-YL]METHYL}-4-(CARBOXYMETHYL)-1H-PYRROL-3- HETNAM 3 DPM YL]PROPANOIC ACID HETNAM ACY ACETIC ACID HETSYN DPM DIPYRROMETHANE COFACTOR FORMUL 2 DPM C20 H24 N2 O8 FORMUL 3 ACY C2 H4 O2 FORMUL 4 HOH *249(H2 O) HELIX 1 1-1 PRO A 14 SER A 30 1 17 HELIX 2 2A1 ARG A 44 VAL A 47 1 4 HELIX 3 2-1 LYS A 64 LEU A 71 1 8 HELIX 4 H1 MET A 82 ASP A 84 5 3 HELIX 5 H2 LEU A 116 ALA A 118 5 3 HELIX 6 1-2 LEU A 130 ARG A 139 1 10 HELIX 7 2-2 VAL A 152 ASP A 160 1 9 HELIX 8 3-2 VAL A 171 ARG A 176 1 6 HELIX 9 H3 GLU A 180 ARG A 182 5 3 HELIX 10 H4 PRO A 189 ILE A 191 5 3 HELIX 11 4-1 SER A 210 ALA A 217 1 8 HELIX 12 H5 ALA A 217 LEU A 219 5 3 HELIX 13 1-3 HIS A 222 LEU A 238 1 17 HELIX 14 H6 PRO A 280 PRO A 280 5 1 HELIX 15 2-3 ALA A 283 ASN A 296 1 14 HELIX 16 3-3 ALA A 299 GLU A 305 1 7 SHEET 1 1 5 VAL A 35 MET A 41 0 SHEET 2 1 5 VAL A 5 THR A 10 1 O LEU A 6 N GLU A 37 SHEET 3 1 5 ILE A 77 SER A 81 1 N ILE A 77 O ARG A 7 SHEET 4 1 5 ALA A 200 ARG A 206 -1 N GLY A 202 O HIS A 80 SHEET 5 1 5 LEU A 93 CYS A 99 -1 N GLY A 94 O CYS A 205 SHEET 1 2 5 ILE A 144 ARG A 146 0 SHEET 2 2 5 ILE A 124 THR A 127 1 N VAL A 125 O ILE A 144 SHEET 3 2 5 ALA A 166 ALA A 170 1 N ALA A 166 O ILE A 124 SHEET 4 2 5 ARG A 105 VAL A 109 -1 O VAL A 109 N ALA A 166 SHEET 5 2 5 ALA A 185 LEU A 187 -1 N LEU A 187 O ASP A 106 SHEET 1 3 3 ILE A 246 ILE A 253 0 SHEET 2 3 3 GLU A 256 ALA A 265 -1 N GLU A 256 O ILE A 253 SHEET 3 3 3 GLN A 270 GLY A 278 -1 O GLN A 270 N ALA A 265 LINK SG CYS A 242 CHA DPM A 314 1555 1555 1.88 SITE 1 DPM 1 CYS A 242 SITE 1 AC1 17 ARG A 11 SER A 13 PHE A 62 LYS A 83 SITE 2 AC1 17 ASP A 84 THR A 127 SER A 128 SER A 129 SITE 3 AC1 17 ARG A 131 ARG A 132 ARG A 149 GLY A 150 SITE 4 AC1 17 ASN A 151 VAL A 152 ARG A 155 CYS A 242 SITE 5 AC1 17 HOH A 402 SITE 1 AC2 5 LYS A 83 ARG A 132 LEU A 169 ALA A 170 SITE 2 AC2 5 HOH A 468 CRYST1 88.000 75.900 50.500 90.00 90.00 90.00 P 21 21 2 4 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 0.011364 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013175 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019802 0.00000