HEADER ISOMERASE 29-MAY-09 3HMK TITLE CRYSTAL STRUCTURE OF SERINE RACEMASE 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_STRAIN: ROSETTA 2(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET24A KEYWDS SERINE RACEMASE, D-SERINE, PYRIDOXAL PHOSPHATE, PLP, NMDA GLUTAMATE KEYWDS 2 RECEPTOR, SCHIZOPHRENIA, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.A.SMITH,J.BARKER,V.MACK,A.EBNETH,B.FELICETTI,M.WOODS REVDAT 5 01-NOV-23 3HMK 1 REMARK REVDAT 4 10-NOV-21 3HMK 1 REMARK SEQADV LINK REVDAT 3 14-FEB-18 3HMK 1 REMARK REVDAT 2 12-MAY-10 3HMK 1 JRNL REVDAT 1 26-JAN-10 3HMK 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. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 32657 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) : 0.244 REMARK 3 R VALUE (WORKING SET) : 0.241 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1795 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1786 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.12 REMARK 3 BIN R VALUE (WORKING SET) : 0.2880 REMARK 3 BIN FREE R VALUE SET COUNT : 99 REMARK 3 BIN FREE R VALUE : 0.3150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4844 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 202 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 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): 0.336 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.248 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.176 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.637 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.920 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.881 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4971 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6775 ; 0.993 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 641 ; 5.242 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 189 ;38.297 ;25.926 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 827 ;14.354 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;19.152 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 813 ; 0.065 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3670 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 3205 ; 0.402 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5204 ; 0.739 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1766 ; 0.771 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1571 ; 1.340 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 3HMK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000053317. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-SEP-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SILICON REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32657 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 41.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 200 DATA REDUNDANCY : 3.170 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : 0.06900 REMARK 200 FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.95 REMARK 200 R MERGE FOR SHELL (I) : 0.19500 REMARK 200 R SYM FOR SHELL (I) : 0.19500 REMARK 200 FOR SHELL : 3.500 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: PDB ENTRY 1FKP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 24.13050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.46150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.48000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.46150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.13050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.48000 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: 2700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 ASP A 2 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 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: 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 THR A 52 -6.64 77.33 REMARK 500 LEU A 67 90.75 -65.63 REMARK 500 PRO A 130 32.03 -73.23 REMARK 500 GLU A 133 -37.42 -161.45 REMARK 500 ASN A 154 -17.59 -145.51 REMARK 500 LYS A 201 79.35 -153.13 REMARK 500 ALA A 214 49.39 -144.35 REMARK 500 THR B 52 -6.97 79.15 REMARK 500 ASP B 70 -55.13 165.03 REMARK 500 LEU B 72 57.33 -93.20 REMARK 500 SER B 83 -92.60 29.39 REMARK 500 SER B 84 -34.65 85.68 REMARK 500 PRO B 130 78.33 -61.51 REMARK 500 SER B 131 30.47 -142.28 REMARK 500 ASP B 132 -79.17 58.41 REMARK 500 ALA B 214 49.99 -149.00 REMARK 500 ASP B 215 32.79 -94.45 REMARK 500 REMARK 500 REMARK: NULL 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 A 340 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 210 OE2 REMARK 620 2 ALA A 214 O 79.1 REMARK 620 3 ASP A 216 OD1 90.1 84.9 REMARK 620 4 HOH A 375 O 86.4 160.0 81.5 REMARK 620 5 HOH A 395 O 167.3 99.5 77.2 91.7 REMARK 620 N 1 2 3 4 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 GLU B 210 OE2 REMARK 620 2 ALA B 214 O 80.4 REMARK 620 3 ASP B 216 OD1 102.0 91.0 REMARK 620 4 HOH B 351 O 93.3 173.3 88.1 REMARK 620 5 HOH B 361 O 171.0 92.7 72.3 93.4 REMARK 620 6 HOH B 394 O 100.8 93.1 157.2 90.3 85.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 340 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP A 350 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 340 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP B 350 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3FDA RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF HUMAN SERINE RACEMASE IN COMPLEX WITH REMARK 900 MALONATE A POTENT INHIBITOR REMARK 900 RELATED ID: 3FKP RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF RAT SERINE RACEMASE IN COMPLEX WITH REMARK 900 MALONATE A POTENT INHIBITOR REMARK 900 RELATED ID: 1V71 RELATED DB: PDB REMARK 900 S.POMBE SERINE RACEMASE REMARK 900 RELATED ID: 1WTC RELATED DB: PDB REMARK 900 S.POMBE SERINE RACEMASE IN COMPLEX WITH AMPPCP DBREF 3HMK A 1 333 UNP Q76EQ0 SRR_RAT 1 333 DBREF 3HMK B 1 333 UNP Q76EQ0 SRR_RAT 1 333 SEQADV 3HMK ASP A 2 UNP Q76EQ0 CYS 2 ENGINEERED MUTATION SEQADV 3HMK ASP A 6 UNP Q76EQ0 CYS 6 ENGINEERED MUTATION SEQADV 3HMK HIS A 334 UNP Q76EQ0 EXPRESSION TAG SEQADV 3HMK HIS A 335 UNP Q76EQ0 EXPRESSION TAG SEQADV 3HMK HIS A 336 UNP Q76EQ0 EXPRESSION TAG SEQADV 3HMK HIS A 337 UNP Q76EQ0 EXPRESSION TAG SEQADV 3HMK HIS A 338 UNP Q76EQ0 EXPRESSION TAG SEQADV 3HMK HIS A 339 UNP Q76EQ0 EXPRESSION TAG SEQADV 3HMK ASP B 2 UNP Q76EQ0 CYS 2 ENGINEERED MUTATION SEQADV 3HMK ASP B 6 UNP Q76EQ0 CYS 6 ENGINEERED MUTATION SEQADV 3HMK HIS B 334 UNP Q76EQ0 EXPRESSION TAG SEQADV 3HMK HIS B 335 UNP Q76EQ0 EXPRESSION TAG SEQADV 3HMK HIS B 336 UNP Q76EQ0 EXPRESSION TAG SEQADV 3HMK HIS B 337 UNP Q76EQ0 EXPRESSION TAG SEQADV 3HMK HIS B 338 UNP Q76EQ0 EXPRESSION TAG SEQADV 3HMK 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 MN A 340 1 HET PLP A 350 15 HET MN B 340 1 HET PLP B 350 15 HETNAM MN MANGANESE (II) ION HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 3 MN 2(MN 2+) FORMUL 4 PLP 2(C8 H10 N O6 P) FORMUL 7 HOH *202(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 LEU A 67 1 12 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 GLU A 133 GLU A 147 1 15 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 SER A 295 1 13 HELIX 16 16 GLN A 296 VAL A 301 5 6 HELIX 17 17 SER B 8 GLN B 20 1 13 HELIX 18 18 SER B 31 GLY B 39 1 9 HELIX 19 19 LEU B 48 PHE B 55 5 8 HELIX 20 20 LYS B 56 GLY B 66 1 11 HELIX 21 21 GLY B 85 GLY B 99 1 15 HELIX 22 22 PRO B 111 ALA B 117 1 7 HELIX 23 23 GLU B 133 GLU B 147 1 15 HELIX 24 24 GLU B 156 VAL B 174 1 19 HELIX 25 25 GLY B 187 LYS B 201 1 15 HELIX 26 26 ASP B 215 GLY B 224 1 10 HELIX 27 27 ALA B 237 LYS B 241 5 5 HELIX 28 28 THR B 248 VAL B 256 1 9 HELIX 29 29 THR B 263 LYS B 279 1 17 HELIX 30 30 GLU B 283 ALA B 286 5 4 HELIX 31 31 GLY B 287 SER B 295 1 9 HELIX 32 32 GLN B 296 VAL B 301 5 6 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 308 N ASN A 41 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 TYR A 207 N LEU A 180 SHEET 6 A 6 ASP A 258 VAL A 262 1 O ASP A 258 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 VAL A 106 O VAL A 126 SHEET 3 B 4 VAL A 79 THR A 81 1 N VAL A 79 O TYR A 103 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 LEU B 29 0 SHEET 2 C 6 ASN B 41 CYS B 46 -1 O PHE B 44 N LEU B 29 SHEET 3 C 6 ASN B 307 LEU B 312 1 O ILE B 308 N ASN B 41 SHEET 4 C 6 ALA B 179 PRO B 183 1 N VAL B 181 O CYS B 309 SHEET 5 C 6 LYS B 205 PRO B 211 1 O TYR B 207 N LEU B 180 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 TYR B 127 0 SHEET 2 D 4 ALA B 102 VAL B 106 1 N ILE B 104 O VAL B 126 SHEET 3 D 4 VAL B 79 THR B 81 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 1.54 LINK NZ LYS B 56 C4A PLP B 350 1555 1555 1.52 LINK OE2 GLU A 210 MN MN A 340 1555 1555 2.13 LINK O ALA A 214 MN MN A 340 1555 1555 2.21 LINK OD1 ASP A 216 MN MN A 340 1555 1555 2.09 LINK MN MN A 340 O HOH A 375 1555 1555 2.04 LINK MN MN A 340 O HOH A 395 1555 1555 2.14 LINK OE2 GLU B 210 MN MN B 340 1555 1555 2.12 LINK O ALA B 214 MN MN B 340 1555 1555 2.21 LINK OD1 ASP B 216 MN MN B 340 1555 1555 2.10 LINK MN MN B 340 O HOH B 351 1555 1555 1.97 LINK MN MN B 340 O HOH B 361 1555 1555 2.20 LINK MN MN B 340 O HOH B 394 1555 1555 2.18 SITE 1 AC1 5 GLU A 210 ALA A 214 ASP A 216 HOH A 375 SITE 2 AC1 5 HOH A 395 SITE 1 AC2 16 PHE A 55 LYS A 56 ASN A 86 GLY A 185 SITE 2 AC2 16 GLY A 186 GLY A 187 GLY A 188 MET A 189 SITE 3 AC2 16 GLY A 239 VAL A 240 THR A 285 SER A 313 SITE 4 AC2 16 GLY A 314 HOH A 346 HOH A 409 HOH A 454 SITE 1 AC3 6 GLU B 210 ALA B 214 ASP B 216 HOH B 351 SITE 2 AC3 6 HOH B 361 HOH B 394 SITE 1 AC4 14 PHE B 55 LYS B 56 ASN B 86 GLY B 185 SITE 2 AC4 14 GLY B 186 GLY B 187 GLY B 188 MET B 189 SITE 3 AC4 14 GLY B 239 GLU B 283 THR B 285 SER B 313 SITE 4 AC4 14 HOH B 421 HOH B 424 CRYST1 48.261 102.960 120.923 90.00 90.00 90.00 P 21 21 21 8 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 0.020721 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009713 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008270 0.00000