HEADER ISOMERASE 18-OCT-16 5M46 TITLE ALPHA-AMINO EPSILON-CAPROLACTAM RACEMASE (ACLR) FROM RHIZOBACTERIUM TITLE 2 FREIREI COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMINOTRANSFERASE CLASS-III; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHIZOBIUM FREIREI PRF 81; SOURCE 3 ORGANISM_TAXID: 363754; SOURCE 4 GENE: RHSP_08934; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET-YSBLIC-3C KEYWDS PLP, RACEMASE, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.FRESE,P.W.SUTTON,J.P.TURKENBURG,G.GROGAN REVDAT 2 17-JAN-24 5M46 1 REMARK REVDAT 1 19-APR-17 5M46 0 JRNL AUTH A.FRESE,P.W.SUTTON,J.P.TURKENBURG,G.GROGAN JRNL TITL SNAPSHOTS OF THE CATALYTIC CYCLE OF THE INDUSTRIAL ENZYME JRNL TITL 2 ALPHA-AMINO-EPSILON-CAPROLACTAM RACEMASE (ACLR) OBSERVED JRNL TITL 3 USING X-RAY CRYSTALLOGRAPHY JRNL REF ACS CATALYSIS V. 7 1045 2017 JRNL REFN ESSN 2155-5435 JRNL DOI 10.1021/ACSCATAL.6B03056 REMARK 2 REMARK 2 RESOLUTION. 1.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.24 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 44637 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2152 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.62 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.65 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8592 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2920 REMARK 3 BIN FREE R VALUE SET COUNT : 150 REMARK 3 BIN FREE R VALUE : 0.2990 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3103 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 239 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.14000 REMARK 3 B22 (A**2) : 0.35000 REMARK 3 B33 (A**2) : -0.23000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.21000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.083 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.084 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.766 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3202 ; 0.022 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3080 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4346 ; 2.131 ; 1.981 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7046 ; 1.402 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 431 ; 5.911 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 118 ;30.889 ;22.542 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 467 ;13.404 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;20.915 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 497 ; 0.213 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3684 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 711 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1718 ; 1.788 ; 1.607 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1717 ; 1.786 ; 1.605 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2145 ; 2.415 ; 2.399 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2146 ; 2.414 ; 2.402 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1484 ; 3.029 ; 1.977 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1484 ; 3.029 ; 1.977 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2200 ; 4.377 ; 2.798 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3653 ; 7.786 ;14.142 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3592 ; 7.725 ;13.885 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5M46 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1200001904. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-15 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97950 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44637 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.620 REMARK 200 RESOLUTION RANGE LOW (A) : 45.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.65 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.62800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2ZUK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MGCL2, 25 % PEG 3350, 0.1 MM REMARK 280 HEPES (PH 7.0)., VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 43.80650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.26350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 43.80650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 38.26350 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 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 A 651 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 837 LIES ON A SPECIAL POSITION. 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 SER A 151 REMARK 465 VAL A 152 REMARK 465 GLN A 153 REMARK 465 ALA A 154 REMARK 465 ASP A 155 REMARK 465 ALA A 156 REMARK 465 ALA A 157 REMARK 465 LYS A 158 REMARK 465 ALA A 434 REMARK 465 GLY A 435 REMARK 465 TRP A 436 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 GLN A -3 CG CD OE1 NE2 REMARK 470 ARG A 123 NH1 NH2 REMARK 470 THR A 128 CG2 REMARK 470 ARG A 222 NE CZ NH1 NH2 REMARK 470 GLU A 283 CG CD OE1 OE2 REMARK 470 GLU A 314 CD OE1 OE2 REMARK 470 GLU A 323 CD OE1 OE2 REMARK 470 LYS A 327 CD CE NZ REMARK 470 GLU A 331 CG CD OE1 OE2 REMARK 470 ARG A 339 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 341 CG CD OE1 OE2 REMARK 470 GLN A 362 CG CD OE1 NE2 REMARK 470 MET A 390 CG SD CE REMARK 470 MET A 397 CE REMARK 470 GLU A 405 CG CD OE1 OE2 REMARK 470 ASP A 406 CG OD1 OD2 REMARK 470 GLN A 417 CG CD OE1 NE2 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 O2 EDO A 503 O HOH A 601 1.51 REMARK 500 C2 EDO A 503 O HOH A 601 1.56 REMARK 500 C1 EDO A 503 O HOH A 601 1.66 REMARK 500 SD MET A 397 O HOH A 838 1.87 REMARK 500 O1 EDO A 503 O HOH A 601 1.87 REMARK 500 OD1 ASP A 176 O HOH A 602 2.10 REMARK 500 O HOH A 705 O HOH A 828 2.10 REMARK 500 O HOH A 604 O HOH A 645 2.12 REMARK 500 NH1 ARG A 330 O HOH A 603 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 612 O HOH A 613 4455 2.17 REMARK 500 O1 EDO A 503 O2 EDO A 504 4444 2.18 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 SER A 289 CB SER A 289 OG -0.087 REMARK 500 GLU A 407 CD GLU A 407 OE2 0.071 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 LEU A 45 CB - CG - CD2 ANGL. DEV. = 12.7 DEGREES REMARK 500 ARG A 91 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 190 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ILE A 214 CG1 - CB - CG2 ANGL. DEV. = -14.0 DEGREES REMARK 500 ARG A 249 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 324 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 324 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 377 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ASP A 416 CB - CG - OD1 ANGL. DEV. = 8.2 DEGREES REMARK 500 ASP A 416 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES 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 SER A 209 -81.89 -78.73 REMARK 500 LEU A 244 68.93 38.31 REMARK 500 ALA A 245 -18.33 83.55 REMARK 500 LYS A 267 -111.30 40.30 REMARK 500 ALA A 367 68.69 -102.47 REMARK 500 LEU A 422 -60.47 -29.65 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 A 839 DISTANCE = 6.14 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PLP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 506 DBREF 5M46 A 1 436 UNP N6UXY4 N6UXY4_9RHIZ 1 436 SEQADV 5M46 GLN A -3 UNP N6UXY4 EXPRESSION TAG SEQADV 5M46 GLY A -2 UNP N6UXY4 EXPRESSION TAG SEQADV 5M46 PRO A -1 UNP N6UXY4 EXPRESSION TAG SEQADV 5M46 ALA A 0 UNP N6UXY4 EXPRESSION TAG SEQRES 1 A 440 GLN GLY PRO ALA MET ALA GLY ASN LEU TYR GLY ARG ASP SEQRES 2 A 440 GLY ALA ALA ILE GLY SER LEU GLN LYS LEU ARG PHE PHE SEQRES 3 A 440 PRO LEU ALA VAL ALA GLY GLY GLN GLY ALA ARG LEU VAL SEQRES 4 A 440 GLU GLU ASP GLY ARG GLU LEU ILE ASP LEU SER GLY ALA SEQRES 5 A 440 TRP GLY ALA ALA SER LEU GLY TYR GLY HIS PRO ALA ILE SEQRES 6 A 440 ILE GLU ALA VAL SER ARG ALA ALA ALA ASN PRO ALA GLY SEQRES 7 A 440 ALA SER ILE LEU SER ALA SER ASN ALA PRO ALA VAL ALA SEQRES 8 A 440 LEU ALA GLU ARG LEU THR ALA SER PHE PRO GLY ARG GLY SEQRES 9 A 440 THR HIS LYS VAL TRP PHE GLY HIS SER GLY SER ASP ALA SEQRES 10 A 440 ASN GLU ALA ALA TYR ARG ALA ILE THR ARG ALA THR GLY SEQRES 11 A 440 ARG THR GLY VAL ILE ALA PHE ILE GLY ALA TYR HIS GLY SEQRES 12 A 440 CYS THR VAL GLY SER MET ALA PHE SER GLY HIS SER VAL SEQRES 13 A 440 GLN ALA ASP ALA ALA LYS ALA ASP GLY LEU ILE LEU LEU SEQRES 14 A 440 PRO TYR PRO ASP PRO TYR ARG PRO TYR GLN ASP ASP PRO SEQRES 15 A 440 THR GLY ASP ALA VAL LEU ALA LEU LEU LYS GLU ARG LEU SEQRES 16 A 440 ALA ALA VAL PRO ALA GLY SER ILE ALA ALA ALA PHE ILE SEQRES 17 A 440 GLU PRO ILE GLN SER ASP GLY GLY LEU ILE VAL PRO PRO SEQRES 18 A 440 ASP GLY PHE LEU ARG LYS PHE ALA ASP ILE CYS ARG ALA SEQRES 19 A 440 HIS GLY ILE SER VAL VAL CYS ASP GLU VAL LYS VAL GLY SEQRES 20 A 440 LEU ALA ARG SER GLY ARG LEU HIS CYS PHE GLU HIS GLU SEQRES 21 A 440 GLY PHE VAL PRO ASP ILE LEU VAL LEU GLY LYS GLY LEU SEQRES 22 A 440 GLY GLY GLY LEU PRO LEU SER ALA VAL ILE ALA PRO ALA SEQRES 23 A 440 GLU ILE LEU ASP CYS ALA SER ALA PHE ALA MET GLN THR SEQRES 24 A 440 LEU HIS GLY ASN PRO VAL CYS ALA ALA ALA GLY LEU ALA SEQRES 25 A 440 VAL LEU GLU THR ILE GLU ALA GLU ASN LEU THR THR ALA SEQRES 26 A 440 ALA GLU ARG LYS GLY LYS LEU LEU ARG GLU GLY LEU ALA SEQRES 27 A 440 ARG LEU ALA GLU ARG HIS GLU LEU ILE GLY ASP ILE ARG SEQRES 28 A 440 GLY ARG GLY LEU ALA CYS GLY VAL GLU LEU VAL ARG ASN SEQRES 29 A 440 ARG GLN SER ARG GLU PRO ALA ARG ALA GLU THR ALA LYS SEQRES 30 A 440 LEU ILE TYR ARG ALA TYR GLU LEU GLY LEU VAL LEU TYR SEQRES 31 A 440 TYR VAL GLY MET ASN GLY ASN VAL LEU GLU MET THR PRO SEQRES 32 A 440 PRO LEU THR MET THR GLU ASP GLU VAL ARG HIS ALA VAL SEQRES 33 A 440 ASN LEU LEU ASP GLN ALA PHE THR GLU LEU SER THR VAL SEQRES 34 A 440 SER ASP THR LEU VAL SER GLN PHE ALA GLY TRP HET PLP A 501 15 HET EDO A 502 4 HET EDO A 503 4 HET EDO A 504 4 HET EDO A 505 4 HET EDO A 506 4 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETSYN PLP VITAMIN B6 PHOSPHATE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 PLP C8 H10 N O6 P FORMUL 3 EDO 5(C2 H6 O2) FORMUL 8 HOH *239(H2 O) HELIX 1 AA1 GLY A -2 GLY A 3 1 6 HELIX 2 AA2 ASN A 4 ILE A 13 1 10 HELIX 3 AA3 GLY A 14 LYS A 18 5 5 HELIX 4 AA4 GLY A 47 ALA A 51 5 5 HELIX 5 AA5 HIS A 58 ASN A 71 1 14 HELIX 6 AA6 ASN A 82 SER A 95 1 14 HELIX 7 AA7 SER A 109 GLY A 126 1 18 HELIX 8 AA8 THR A 141 ALA A 146 1 6 HELIX 9 AA9 PRO A 173 ASP A 177 5 5 HELIX 10 AB1 GLY A 180 ALA A 192 1 13 HELIX 11 AB2 GLY A 219 HIS A 231 1 13 HELIX 12 AB3 HIS A 251 GLU A 256 5 6 HELIX 13 AB4 GLY A 266 GLY A 271 5 6 HELIX 14 AB5 ALA A 282 ASP A 286 1 5 HELIX 15 AB6 ASN A 299 GLU A 316 1 18 HELIX 16 AB7 ASN A 317 HIS A 340 1 24 HELIX 17 AB8 ALA A 367 GLY A 382 1 16 HELIX 18 AB9 THR A 404 LEU A 422 1 19 HELIX 19 AC1 SER A 423 VAL A 425 5 3 HELIX 20 AC2 SER A 426 GLN A 432 1 7 SHEET 1 AA1 4 VAL A 26 GLN A 30 0 SHEET 2 AA1 4 ARG A 33 GLU A 36 -1 O VAL A 35 N ALA A 27 SHEET 3 AA1 4 GLU A 41 ASP A 44 -1 O LEU A 42 N LEU A 34 SHEET 4 AA1 4 LEU A 383 VAL A 384 1 O VAL A 384 N ILE A 43 SHEET 1 AA2 7 HIS A 102 GLY A 107 0 SHEET 2 AA2 7 SER A 276 PRO A 281 -1 O ALA A 280 N LYS A 103 SHEET 3 AA2 7 ILE A 262 LEU A 265 -1 N LEU A 265 O ALA A 277 SHEET 4 AA2 7 SER A 234 ASP A 238 1 N CYS A 237 O ILE A 262 SHEET 5 AA2 7 ILE A 199 ILE A 204 1 N ALA A 202 O VAL A 236 SHEET 6 AA2 7 GLY A 129 PHE A 133 1 N ILE A 131 O PHE A 203 SHEET 7 AA2 7 LEU A 162 LEU A 165 1 O ILE A 163 N VAL A 130 SHEET 1 AA3 4 ILE A 343 ARG A 349 0 SHEET 2 AA3 4 ALA A 352 LEU A 357 -1 O GLY A 354 N ARG A 347 SHEET 3 AA3 4 VAL A 394 MET A 397 -1 O MET A 397 N CYS A 353 SHEET 4 AA3 4 TYR A 386 VAL A 388 -1 N TYR A 386 O GLU A 396 LINK NZ LYS A 267 C4A PLP A 501 1555 1555 1.26 SITE 1 AC1 15 SER A 109 GLY A 110 SER A 111 TYR A 137 SITE 2 AC1 15 HIS A 138 GLU A 205 ASP A 238 VAL A 240 SITE 3 AC1 15 LYS A 241 LYS A 267 GLN A 294 THR A 295 SITE 4 AC1 15 HOH A 621 HOH A 628 HOH A 668 SITE 1 AC2 7 PRO A 195 ALA A 196 GLY A 197 SER A 198 SITE 2 AC2 7 ILE A 199 HIS A 231 HOH A 607 SITE 1 AC3 10 LYS A 188 LEU A 191 ALA A 192 HIS A 231 SITE 2 AC3 10 THR A 319 THR A 320 EDO A 504 HOH A 601 SITE 3 AC3 10 HOH A 629 HOH A 656 SITE 1 AC4 8 ALA A 192 HIS A 231 GLY A 248 ARG A 249 SITE 2 AC4 8 THR A 320 EDO A 503 HOH A 601 HOH A 772 SITE 1 AC5 5 SER A 209 LYS A 241 LYS A 267 GLU A 396 SITE 2 AC5 5 HOH A 742 SITE 1 AC6 8 ARG A 172 GLU A 356 GLY A 389 MET A 390 SITE 2 AC6 8 ASN A 391 ASN A 393 VAL A 394 HOH A 642 CRYST1 87.613 76.527 58.570 90.00 113.12 90.00 C 1 2 1 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 0.011414 0.000000 0.004872 0.00000 SCALE2 0.000000 0.013067 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018564 0.00000