HEADER ISOMERASE 23-DEC-09 3L6C TITLE X-RAY CRYSTAL STRUCTURE OF RAT SERINE RACEMASE IN COMPLEX WITH TITLE 2 MALONATE A POTENT INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE RACEMASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 5.1.1.18; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: SRR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET 24C KEYWDS PYRIDOXAL PHOSPHATE, PLP, SERINE RACEMASE, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.A.SMITH,V.MACK,A.EBNETH,I.MORAES,B.FELICETTI,M.WOOD,D.SCHONFELD, AUTHOR 2 O.MATHER,A.CESURA,J.BARKER REVDAT 2 12-MAY-10 3L6C 1 JRNL REVDAT 1 26-JAN-10 3L6C 0 JRNL AUTH M.A.SMITH,V.MACK,A.EBNETH,I.MORAES,B.FELICETTI,M.WOOD, JRNL AUTH 2 D.SCHONFELD,O.MATHER,A.CESURA,J.BARKER JRNL TITL THE STRUCTURE OF MAMMALIAN SERINE RACEMASE: EVIDENCE FOR JRNL TITL 2 CONFORMATIONAL CHANGES UPON INHIBITOR BINDING. JRNL REF J.BIOL.CHEM. V. 285 12873 2010 JRNL REFN ISSN 0021-9258 JRNL PMID 20106978 JRNL DOI 10.1074/JBC.M109.050062 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.500 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 30285 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) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1586 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1655 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 71.34 REMARK 3 BIN R VALUE (WORKING SET) : 0.3290 REMARK 3 BIN FREE R VALUE SET COUNT : 102 REMARK 3 BIN FREE R VALUE : 0.4020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4779 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 80 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : -0.04000 REMARK 3 B33 (A**2) : 0.07000 REMARK 3 B12 (A**2) : -0.02000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.332 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.244 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.194 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.800 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4901 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6676 ; 1.604 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 629 ; 6.844 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 188 ;40.731 ;25.904 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 811 ;17.685 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;17.842 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 798 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3626 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2298 ; 0.214 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3346 ; 0.300 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 188 ; 0.162 ; 0.200 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): 55 ; 0.221 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.064 ; 0.200 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): 3231 ; 0.806 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5111 ; 1.417 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1867 ; 1.983 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1565 ; 3.071 ; 4.500 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 : MASK 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 3L6C COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JAN-10. REMARK 100 THE RCSB ID CODE IS RCSB056888. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54187 REMARK 200 MONOCHROMATOR : RIGAKU VARIMAX OPTICS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30389 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 55.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : 0.06000 REMARK 200 FOR THE DATA SET : 9.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.4 REMARK 200 DATA REDUNDANCY IN SHELL : 1.55 REMARK 200 R MERGE FOR SHELL (I) : 0.31100 REMARK 200 R SYM FOR SHELL (I) : 0.31100 REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: HUMAN SERINE RACEMASE SOLVED BY SELENOMETHIONINE REMARK 200 SAD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,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 -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 0.00000 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 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: 1400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 TRP A 324 REMARK 465 VAL A 325 REMARK 465 LYS A 326 REMARK 465 GLN A 327 REMARK 465 ALA A 328 REMARK 465 GLU A 329 REMARK 465 ARG A 330 REMARK 465 PRO A 331 REMARK 465 ALA A 332 REMARK 465 PRO A 333 REMARK 465 HIS A 334 REMARK 465 HIS A 335 REMARK 465 HIS A 336 REMARK 465 HIS A 337 REMARK 465 HIS A 338 REMARK 465 HIS A 339 REMARK 465 MET B 1 REMARK 465 ASP B 2 REMARK 465 ALA B 3 REMARK 465 LEU B 67 REMARK 465 ILE B 68 REMARK 465 PRO B 69 REMARK 465 ASP B 70 REMARK 465 THR B 71 REMARK 465 LEU B 72 REMARK 465 GLU B 73 REMARK 465 GLY B 74 REMARK 465 LYS B 75 REMARK 465 VAL B 325 REMARK 465 LYS B 326 REMARK 465 GLN B 327 REMARK 465 ALA B 328 REMARK 465 GLU B 329 REMARK 465 ARG B 330 REMARK 465 PRO B 331 REMARK 465 ALA B 332 REMARK 465 PRO B 333 REMARK 465 HIS B 334 REMARK 465 HIS B 335 REMARK 465 HIS B 336 REMARK 465 HIS B 337 REMARK 465 HIS B 338 REMARK 465 HIS B 339 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 ND2 ASN B 154 CA GLY B 186 2.06 REMARK 500 OG SER B 83 O9 MLI B 341 2.17 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 ASP A 216 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 LEU B 48 CA - CB - CG ANGL. DEV. = 16.6 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 PRO A 69 -169.28 -79.87 REMARK 500 ASN A 154 -7.41 -153.51 REMARK 500 ALA A 214 49.03 -149.15 REMARK 500 ASP A 215 41.04 -91.71 REMARK 500 PRO A 232 128.51 -37.11 REMARK 500 THR B 52 -15.44 77.46 REMARK 500 SER B 131 148.47 -170.51 REMARK 500 ASP B 132 -16.88 -49.81 REMARK 500 GLU B 136 1.88 -58.51 REMARK 500 ASN B 137 -52.15 -123.86 REMARK 500 VAL B 138 -9.48 -58.02 REMARK 500 ASN B 154 -14.11 -151.52 REMARK 500 LYS B 201 117.97 -160.93 REMARK 500 ALA B 214 54.41 -142.58 REMARK 500 ASP B 215 36.20 -97.44 REMARK 500 PRO B 303 -6.44 -58.86 REMARK 500 LEU B 322 1.86 -64.94 REMARK 500 SER B 323 25.55 48.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 THR B 52 23.9 L L OUTSIDE RANGE 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 B 358 DISTANCE = 8.06 ANGSTROMS REMARK 525 HOH A 398 DISTANCE = 7.12 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 MN B 340 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 216 OD1 REMARK 620 2 GLU B 210 OE2 100.4 REMARK 620 3 ALA B 214 O 99.9 72.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 340 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 210 OE2 REMARK 620 2 ALA A 214 O 84.2 REMARK 620 3 ASP A 216 OD1 100.4 100.8 REMARK 620 4 HOH A 389 O 96.6 168.0 67.2 REMARK 620 5 HOH A 388 O 109.7 88.6 149.3 102.3 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 PLP A 350 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 340 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MLI A 341 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP B 350 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 340 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MLI B 341 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3L6B RELATED DB: PDB REMARK 900 HUMAN SERINE RACEMASE REMARK 900 RELATED ID: 3L6R RELATED DB: PDB DBREF 3L6C A 1 333 UNP Q76EQ0 SRR_RAT 1 333 DBREF 3L6C B 1 333 UNP Q76EQ0 SRR_RAT 1 333 SEQADV 3L6C ASP A 2 UNP Q76EQ0 CYS 2 ENGINEERED SEQADV 3L6C ASP A 6 UNP Q76EQ0 CYS 6 ENGINEERED SEQADV 3L6C HIS A 334 UNP Q76EQ0 EXPRESSION TAG SEQADV 3L6C HIS A 335 UNP Q76EQ0 EXPRESSION TAG SEQADV 3L6C HIS A 336 UNP Q76EQ0 EXPRESSION TAG SEQADV 3L6C HIS A 337 UNP Q76EQ0 EXPRESSION TAG SEQADV 3L6C HIS A 338 UNP Q76EQ0 EXPRESSION TAG SEQADV 3L6C HIS A 339 UNP Q76EQ0 EXPRESSION TAG SEQADV 3L6C ASP B 2 UNP Q76EQ0 CYS 2 ENGINEERED SEQADV 3L6C ASP B 6 UNP Q76EQ0 CYS 6 ENGINEERED SEQADV 3L6C HIS B 334 UNP Q76EQ0 EXPRESSION TAG SEQADV 3L6C HIS B 335 UNP Q76EQ0 EXPRESSION TAG SEQADV 3L6C HIS B 336 UNP Q76EQ0 EXPRESSION TAG SEQADV 3L6C HIS B 337 UNP Q76EQ0 EXPRESSION TAG SEQADV 3L6C HIS B 338 UNP Q76EQ0 EXPRESSION TAG SEQADV 3L6C HIS B 339 UNP Q76EQ0 EXPRESSION TAG SEQRES 1 A 339 MET ASP ALA GLN TYR ASP ILE SER PHE ALA ASP VAL GLU SEQRES 2 A 339 LYS ALA HIS LEU ASN ILE GLN ASP SER VAL HIS LEU THR SEQRES 3 A 339 PRO VAL LEU THR SER SER ILE LEU ASN GLN ILE ALA GLY SEQRES 4 A 339 ARG ASN LEU PHE PHE LYS CYS GLU LEU PHE GLN LYS THR SEQRES 5 A 339 GLY SER PHE LYS ILE ARG GLY ALA LEU ASN ALA ILE ARG SEQRES 6 A 339 GLY LEU ILE PRO ASP THR LEU GLU GLY LYS PRO LYS ALA SEQRES 7 A 339 VAL VAL THR HIS SER SER GLY ASN HIS GLY GLN ALA LEU SEQRES 8 A 339 THR TYR ALA ALA LYS LEU GLU GLY ILE PRO ALA TYR ILE SEQRES 9 A 339 VAL VAL PRO GLN THR ALA PRO ASN CYS LYS LYS LEU ALA SEQRES 10 A 339 ILE GLN ALA TYR GLY ALA SER ILE VAL TYR SER GLU PRO SEQRES 11 A 339 SER ASP GLU SER ARG GLU ASN VAL ALA GLN ARG ILE ILE SEQRES 12 A 339 GLN GLU THR GLU GLY ILE LEU VAL HIS PRO ASN GLN GLU SEQRES 13 A 339 PRO ALA VAL ILE ALA GLY GLN GLY THR ILE ALA LEU GLU SEQRES 14 A 339 VAL LEU ASN GLN VAL PRO LEU VAL ASP ALA LEU VAL VAL SEQRES 15 A 339 PRO VAL GLY GLY GLY GLY MET VAL ALA GLY ILE ALA ILE SEQRES 16 A 339 THR ILE LYS THR LEU LYS PRO SER VAL LYS VAL TYR ALA SEQRES 17 A 339 ALA GLU PRO SER ASN ALA ASP ASP CYS TYR GLN SER LYS SEQRES 18 A 339 LEU LYS GLY GLU LEU THR PRO ASN LEU HIS PRO PRO GLU SEQRES 19 A 339 THR ILE ALA ASP GLY VAL LYS SER SER ILE GLY LEU ASN SEQRES 20 A 339 THR TRP PRO ILE ILE ARG ASP LEU VAL ASP ASP VAL PHE SEQRES 21 A 339 THR VAL THR GLU ASP GLU ILE LYS TYR ALA THR GLN LEU SEQRES 22 A 339 VAL TRP GLU ARG MET LYS LEU LEU ILE GLU PRO THR ALA SEQRES 23 A 339 GLY VAL GLY LEU ALA ALA VAL LEU SER GLN HIS PHE GLN SEQRES 24 A 339 THR VAL SER PRO GLU VAL LYS ASN ILE CYS ILE VAL LEU SEQRES 25 A 339 SER GLY GLY ASN VAL ASP LEU THR SER LEU SER TRP VAL SEQRES 26 A 339 LYS GLN ALA GLU ARG PRO ALA PRO HIS HIS HIS HIS HIS SEQRES 27 A 339 HIS SEQRES 1 B 339 MET ASP ALA GLN TYR ASP ILE SER PHE ALA ASP VAL GLU SEQRES 2 B 339 LYS ALA HIS LEU ASN ILE GLN ASP SER VAL HIS LEU THR SEQRES 3 B 339 PRO VAL LEU THR SER SER ILE LEU ASN GLN ILE ALA GLY SEQRES 4 B 339 ARG ASN LEU PHE PHE LYS CYS GLU LEU PHE GLN LYS THR SEQRES 5 B 339 GLY SER PHE LYS ILE ARG GLY ALA LEU ASN ALA ILE ARG SEQRES 6 B 339 GLY LEU ILE PRO ASP THR LEU GLU GLY LYS PRO LYS ALA SEQRES 7 B 339 VAL VAL THR HIS SER SER GLY ASN HIS GLY GLN ALA LEU SEQRES 8 B 339 THR TYR ALA ALA LYS LEU GLU GLY ILE PRO ALA TYR ILE SEQRES 9 B 339 VAL VAL PRO GLN THR ALA PRO ASN CYS LYS LYS LEU ALA SEQRES 10 B 339 ILE GLN ALA TYR GLY ALA SER ILE VAL TYR SER GLU PRO SEQRES 11 B 339 SER ASP GLU SER ARG GLU ASN VAL ALA GLN ARG ILE ILE SEQRES 12 B 339 GLN GLU THR GLU GLY ILE LEU VAL HIS PRO ASN GLN GLU SEQRES 13 B 339 PRO ALA VAL ILE ALA GLY GLN GLY THR ILE ALA LEU GLU SEQRES 14 B 339 VAL LEU ASN GLN VAL PRO LEU VAL ASP ALA LEU VAL VAL SEQRES 15 B 339 PRO VAL GLY GLY GLY GLY MET VAL ALA GLY ILE ALA ILE SEQRES 16 B 339 THR ILE LYS THR LEU LYS PRO SER VAL LYS VAL TYR ALA SEQRES 17 B 339 ALA GLU PRO SER ASN ALA ASP ASP CYS TYR GLN SER LYS SEQRES 18 B 339 LEU LYS GLY GLU LEU THR PRO ASN LEU HIS PRO PRO GLU SEQRES 19 B 339 THR ILE ALA ASP GLY VAL LYS SER SER ILE GLY LEU ASN SEQRES 20 B 339 THR TRP PRO ILE ILE ARG ASP LEU VAL ASP ASP VAL PHE SEQRES 21 B 339 THR VAL THR GLU ASP GLU ILE LYS TYR ALA THR GLN LEU SEQRES 22 B 339 VAL TRP GLU ARG MET LYS LEU LEU ILE GLU PRO THR ALA SEQRES 23 B 339 GLY VAL GLY LEU ALA ALA VAL LEU SER GLN HIS PHE GLN SEQRES 24 B 339 THR VAL SER PRO GLU VAL LYS ASN ILE CYS ILE VAL LEU SEQRES 25 B 339 SER GLY GLY ASN VAL ASP LEU THR SER LEU SER TRP VAL SEQRES 26 B 339 LYS GLN ALA GLU ARG PRO ALA PRO HIS HIS HIS HIS HIS SEQRES 27 B 339 HIS HET PLP A 350 15 HET MN A 340 1 HET MLI A 341 7 HET PLP B 350 15 HET MN B 340 1 HET MLI B 341 7 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM MLI MALONATE ION HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 3 PLP 2(C8 H10 N O6 P) FORMUL 4 MN 2(MN 2+) FORMUL 5 MLI 2(C3 H2 O4 2-) FORMUL 9 HOH *80(H2 O) HELIX 1 1 SER A 8 GLN A 20 1 13 HELIX 2 2 SER A 31 GLY A 39 1 9 HELIX 3 3 LEU A 48 PHE A 55 5 8 HELIX 4 4 LYS A 56 ILE A 68 1 13 HELIX 5 5 GLY A 85 GLU A 98 1 14 HELIX 6 6 PRO A 111 TYR A 121 1 11 HELIX 7 7 SER A 131 GLU A 147 1 17 HELIX 8 8 GLU A 156 GLY A 164 1 9 HELIX 9 9 GLY A 164 VAL A 174 1 11 HELIX 10 10 GLY A 187 LYS A 201 1 15 HELIX 11 11 ASP A 215 GLY A 224 1 10 HELIX 12 12 ALA A 237 LYS A 241 5 5 HELIX 13 13 THR A 248 VAL A 256 1 9 HELIX 14 14 THR A 263 LYS A 279 1 17 HELIX 15 15 GLU A 283 ALA A 286 5 4 HELIX 16 16 GLY A 287 LEU A 294 1 8 HELIX 17 17 GLN A 296 VAL A 301 5 6 HELIX 18 18 SER B 8 GLN B 20 1 13 HELIX 19 19 SER B 31 GLY B 39 1 9 HELIX 20 20 LEU B 48 PHE B 55 5 8 HELIX 21 21 LYS B 56 ARG B 65 1 10 HELIX 22 22 ASN B 86 LEU B 97 1 12 HELIX 23 23 PRO B 111 TYR B 121 1 11 HELIX 24 24 SER B 131 GLU B 147 1 17 HELIX 25 25 GLU B 156 GLN B 163 1 8 HELIX 26 26 GLY B 164 VAL B 174 1 11 HELIX 27 27 GLY B 187 LYS B 201 1 15 HELIX 28 28 ASP B 215 GLY B 224 1 10 HELIX 29 29 ALA B 237 LYS B 241 5 5 HELIX 30 30 ASN B 247 VAL B 256 1 10 HELIX 31 31 THR B 263 ARG B 277 1 15 HELIX 32 32 GLU B 283 THR B 285 5 3 HELIX 33 33 ALA B 286 LEU B 294 1 9 HELIX 34 34 HIS B 297 VAL B 301 5 5 SHEET 1 A 6 VAL A 28 LEU A 29 0 SHEET 2 A 6 ASN A 41 CYS A 46 -1 O PHE A 44 N LEU A 29 SHEET 3 A 6 ASN A 307 LEU A 312 1 O ILE A 310 N PHE A 43 SHEET 4 A 6 ALA A 179 PRO A 183 1 N ALA A 179 O CYS A 309 SHEET 5 A 6 LYS A 205 PRO A 211 1 O LYS A 205 N LEU A 180 SHEET 6 A 6 ASP A 258 VAL A 262 1 O PHE A 260 N ALA A 208 SHEET 1 B 4 SER A 124 SER A 128 0 SHEET 2 B 4 ALA A 102 PRO A 107 1 N ILE A 104 O SER A 124 SHEET 3 B 4 VAL A 79 HIS A 82 1 N THR A 81 O VAL A 105 SHEET 4 B 4 ILE A 149 LEU A 150 1 O ILE A 149 N VAL A 80 SHEET 1 C 6 VAL B 28 THR B 30 0 SHEET 2 C 6 PHE B 43 CYS B 46 -1 O PHE B 44 N LEU B 29 SHEET 3 C 6 ILE B 308 LEU B 312 1 O ILE B 308 N PHE B 43 SHEET 4 C 6 ALA B 179 PRO B 183 1 N ALA B 179 O CYS B 309 SHEET 5 C 6 LYS B 205 PRO B 211 1 O TYR B 207 N VAL B 182 SHEET 6 C 6 ASP B 258 VAL B 262 1 O PHE B 260 N ALA B 208 SHEET 1 D 4 SER B 124 SER B 128 0 SHEET 2 D 4 ALA B 102 PRO B 107 1 N ILE B 104 O SER B 124 SHEET 3 D 4 VAL B 79 HIS B 82 1 N THR B 81 O VAL B 105 SHEET 4 D 4 ILE B 149 LEU B 150 1 O ILE B 149 N VAL B 80 LINK NZ LYS A 56 C4A PLP A 350 1555 1555 1.28 LINK NZ LYS B 56 C4A PLP B 350 1555 1555 1.26 LINK OD1 ASP B 216 MN MN B 340 1555 1555 1.93 LINK OE2 GLU A 210 MN MN A 340 1555 1555 1.93 LINK O ALA A 214 MN MN A 340 1555 1555 1.95 LINK OD1 ASP A 216 MN MN A 340 1555 1555 1.96 LINK OE2 GLU B 210 MN MN B 340 1555 1555 2.29 LINK MN MN A 340 O HOH A 389 1555 1555 2.46 LINK O ALA B 214 MN MN B 340 1555 1555 2.51 LINK MN MN A 340 O HOH A 388 1555 1555 2.64 SITE 1 AC1 17 PHE A 55 LYS A 56 ASN A 86 ASN A 154 SITE 2 AC1 17 GLY A 185 GLY A 186 GLY A 187 GLY A 188 SITE 3 AC1 17 MET A 189 GLY A 239 VAL A 240 THR A 285 SITE 4 AC1 17 SER A 313 MLI A 341 HOH A 346 HOH A 355 SITE 5 AC1 17 HOH A 358 SITE 1 AC2 5 GLU A 210 ALA A 214 ASP A 216 HOH A 388 SITE 2 AC2 5 HOH A 389 SITE 1 AC3 11 LYS A 56 SER A 83 SER A 84 ASN A 86 SITE 2 AC3 11 HIS A 87 ARG A 135 SER A 242 PLP A 350 SITE 3 AC3 11 HOH A 355 HOH A 365 HOH A 393 SITE 1 AC4 14 PHE B 55 LYS B 56 ASN B 86 PRO B 183 SITE 2 AC4 14 VAL B 184 GLY B 185 GLY B 186 GLY B 187 SITE 3 AC4 14 GLY B 188 MET B 189 GLU B 283 THR B 285 SITE 4 AC4 14 SER B 313 HOH B 345 SITE 1 AC5 3 GLU B 210 ALA B 214 ASP B 216 SITE 1 AC6 9 LYS B 56 SER B 83 SER B 84 GLY B 85 SITE 2 AC6 9 ASN B 86 HIS B 87 ARG B 135 GLY B 239 SITE 3 AC6 9 SER B 242 CRYST1 110.593 110.593 47.917 90.00 90.00 120.00 P 3 6 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 0.009042 0.005220 0.000000 0.00000 SCALE2 0.000000 0.010441 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020869 0.00000 MASTER 431 0 6 34 20 0 18 6 0 0 0 54 END