HEADER TRANSFERASE 24-APR-12 3VSD TITLE CRYSTAL STRUCTURE OF THE K127A MUTANT OF O-PHOSPHOSERINE SULFHYDRYLASE TITLE 2 COMPLEXED WITH EXTERNAL SCHIFF BASE OF PYRIDOXAL 5'-PHOSPHATE WITH O- TITLE 3 ACETYL-L-SERINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN CYSO; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CYSTATHIONINE BETA-SYNTHASE, CYSTEINE SYNTHASE, O- COMPND 5 ACETYLSERINE SULFHYDRYLASE, O-PHOSPHOSERINE SULFHYDRYLASE, SERINE COMPND 6 SULFHYDRASE; COMPND 7 EC: 4.2.1.22, 2.5.1.47, 2.5.1.65; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AEROPYRUM PERNIX; SOURCE 3 ORGANISM_TAXID: 272557; SOURCE 4 STRAIN: K1; SOURCE 5 GENE: APE1586, APE_1586, CYSO; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET3D KEYWDS CYSTEINE BIOSYNTHESIS, EXTERNAL SCHIFF BASE OF PLP WITH O- KEYWDS 2 ACETYLSERINE, K127A MUTANT, SULFHYDRYLASE (INACTIVATED), TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR T.NAKAMURA,Y.KAWAI,M.KATAOKA,K.ISHIKAWA REVDAT 3 22-NOV-17 3VSD 1 REMARK REVDAT 2 16-MAR-16 3VSD 1 JRNL REVDAT 1 16-MAY-12 3VSD 0 JRNL AUTH T.NAKAMURA,Y.KAWAI,K.KUNIMOTO,Y.IWASAKI,K.NISHII,M.KATAOKA, JRNL AUTH 2 K.ISHIKAWA JRNL TITL STRUCTURAL ANALYSIS OF THE SUBSTRATE RECOGNITION MECHANISM JRNL TITL 2 IN O-PHOSPHOSERINE SULFHYDRYLASE FROM THE HYPERTHERMOPHILIC JRNL TITL 3 ARCHAEON AEROPYRUM PERNIX K1 JRNL REF J.MOL.BIOL. V. 422 33 2012 JRNL REFN ISSN 0022-2836 JRNL PMID 22580223 JRNL DOI 10.1016/J.JMB.2012.05.009 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.ODA,K.MINO,K.ISHIKAWA,M.ATAKA REMARK 1 TITL THREE-DIMENSIONAL STRUCTURE OF A NEW ENZYME, O-PHOSPHOSERINE REMARK 1 TITL 2 SULFHYDRYLASE, INVOLVED IN L-CYSTEINE BIOSYNTHESIS BY A REMARK 1 TITL 3 HYPERTHERMOPHILIC ARCHAEON, AEROPYRUM PERNIX K1, AT 2.0A REMARK 1 TITL 4 RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 351 334 2005 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 16005886 REMARK 1 DOI 10.1016/J.JMB.2005.05.064 REMARK 2 REMARK 2 RESOLUTION. 2.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 47256 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) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.305 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2386 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) : 2.09 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3092 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.38 REMARK 3 BIN R VALUE (WORKING SET) : 0.4500 REMARK 3 BIN FREE R VALUE SET COUNT : 181 REMARK 3 BIN FREE R VALUE : 0.4760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5826 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 99 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.43000 REMARK 3 B22 (A**2) : 2.43000 REMARK 3 B33 (A**2) : -4.85000 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): 0.270 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.240 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.206 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.259 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6052 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8227 ; 1.867 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 773 ; 7.337 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 258 ;34.869 ;22.791 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 971 ;19.433 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 58 ;21.728 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 920 ; 0.125 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4642 ; 0.009 ; 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): 3836 ; 0.942 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6157 ; 1.661 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2216 ; 2.646 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2070 ; 4.131 ; 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 : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 3VSD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000095440. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUL-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.90000 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : RHODIUM-COATED MIRROR REMARK 200 (HORIZONTAL) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER DIP-6040 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47287 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.090 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.33500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC 5.5.0109 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES SODIUM PH 6.8, 27% 2 REMARK 280 -PROPANOL, 10% PEG 4000, 5MM O-ACETYL-L-SERINE, 5MM 2- REMARK 280 MERCAPTOETHANOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 137.89200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 37.82300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 37.82300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 206.83800 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 37.82300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 37.82300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 68.94600 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 37.82300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.82300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 206.83800 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 37.82300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.82300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 68.94600 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 137.89200 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 GLY A 384 REMARK 465 ALA A 385 REMARK 465 GLY A 386 REMARK 465 ASP A 387 REMARK 465 SER A 388 REMARK 465 VAL A 389 REMARK 465 MET B 1 REMARK 465 ALA B 385 REMARK 465 GLY B 386 REMARK 465 ASP B 387 REMARK 465 SER B 388 REMARK 465 VAL B 389 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 OD1 ASP A 5 OG SER A 7 2.12 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 PRO A 98 C - N - CA ANGL. DEV. = 9.1 DEGREES REMARK 500 ARG B 26 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 PRO B 40 C - N - CA ANGL. DEV. = 11.0 DEGREES REMARK 500 LEU B 138 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 ILE A 134 -71.32 -62.37 REMARK 500 SER A 136 -45.65 -27.47 REMARK 500 LYS A 144 154.05 -46.74 REMARK 500 SER A 154 -54.11 162.71 REMARK 500 PRO A 201 21.10 -77.11 REMARK 500 SER A 202 168.47 171.22 REMARK 500 ASN A 223 83.20 40.52 REMARK 500 SER A 263 -0.96 84.13 REMARK 500 LEU A 304 -78.60 -63.25 REMARK 500 PHE B 122 -66.53 -94.73 REMARK 500 ARG B 140 -70.85 -61.46 REMARK 500 SER B 154 -52.14 168.84 REMARK 500 ALA B 200 109.57 -31.86 REMARK 500 SER B 202 159.93 175.71 REMARK 500 ASN B 223 78.63 31.38 REMARK 500 SER B 263 5.46 86.64 REMARK 500 ALA B 288 133.09 -37.77 REMARK 500 LEU B 304 -79.92 -65.30 REMARK 500 TYR B 374 56.48 -117.80 REMARK 500 GLU B 383 59.25 -105.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU B 300 THR B 301 147.65 REMARK 500 REMARK 500 REMARK: NULL 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OAS A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OAS B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WKV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF O-PHOSPHOSERINE SULFHYDRYLASE REMARK 900 RELATED ID: 3VSA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF O-PHOSPHOSERINE SULFHYDRYLASE WITHOUT ACETATE REMARK 900 RELATED ID: 3VSC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE K127A MUTANT OF O-PHOSPHOSERINE REMARK 900 SULFHYDRYLASE COMPLEXED WITH EXTERNAL SCHIFF BASE OF PYRIDOXAL 5'- REMARK 900 PHOSPHATE WITH O-PHOSPHO-L-SERINE DBREF 3VSD A 1 389 UNP Q9YBL2 CYSO_AERPE 1 389 DBREF 3VSD B 1 389 UNP Q9YBL2 CYSO_AERPE 1 389 SEQADV 3VSD ALA A 127 UNP Q9YBL2 LYS 127 ENGINEERED MUTATION SEQADV 3VSD ALA B 127 UNP Q9YBL2 LYS 127 ENGINEERED MUTATION SEQRES 1 A 389 MET ALA LEU ALA ASP ILE SER GLY TYR LEU ASP VAL LEU SEQRES 2 A 389 ASP SER VAL ARG GLY PHE SER TYR LEU GLU ASN ALA ARG SEQRES 3 A 389 GLU VAL LEU ARG SER GLY GLU ALA ARG CYS LEU GLY ASN SEQRES 4 A 389 PRO ARG SER GLU PRO GLU TYR VAL LYS ALA LEU TYR VAL SEQRES 5 A 389 ILE GLY ALA SER ARG ILE PRO VAL GLY ASP GLY CYS SER SEQRES 6 A 389 HIS THR LEU GLU GLU LEU GLY VAL PHE ASP ILE SER VAL SEQRES 7 A 389 PRO GLY GLU MET VAL PHE PRO SER PRO LEU ASP PHE PHE SEQRES 8 A 389 GLU ARG GLY LYS PRO THR PRO LEU VAL ARG SER ARG LEU SEQRES 9 A 389 GLN LEU PRO ASN GLY VAL ARG VAL TRP LEU LYS LEU GLU SEQRES 10 A 389 TRP TYR ASN PRO PHE SER LEU SER VAL ALA ASP ARG PRO SEQRES 11 A 389 ALA VAL GLU ILE ILE SER ARG LEU SER ARG ARG VAL GLU SEQRES 12 A 389 LYS GLY SER LEU VAL ALA ASP ALA THR SER SER ASN PHE SEQRES 13 A 389 GLY VAL ALA LEU SER ALA VAL ALA ARG LEU TYR GLY TYR SEQRES 14 A 389 ARG ALA ARG VAL TYR LEU PRO GLY ALA ALA GLU GLU PHE SEQRES 15 A 389 GLY LYS LEU LEU PRO ARG LEU LEU GLY ALA GLN VAL ILE SEQRES 16 A 389 VAL ASP PRO GLU ALA PRO SER THR VAL HIS LEU LEU PRO SEQRES 17 A 389 ARG VAL MET LYS ASP SER LYS ASN GLU GLY PHE VAL HIS SEQRES 18 A 389 VAL ASN GLN PHE TYR ASN ASP ALA ASN PHE GLU ALA HIS SEQRES 19 A 389 MET ARG GLY THR ALA ARG GLU ILE PHE VAL GLN SER ARG SEQRES 20 A 389 ARG GLY GLY LEU ALA LEU ARG GLY VAL ALA GLY SER LEU SEQRES 21 A 389 GLY THR SER GLY HIS MET SER ALA ALA ALA PHE TYR LEU SEQRES 22 A 389 GLN SER VAL ASP PRO SER ILE ARG ALA VAL LEU VAL GLN SEQRES 23 A 389 PRO ALA GLN GLY ASP SER ILE PRO GLY ILE ARG ARG VAL SEQRES 24 A 389 GLU THR GLY MET LEU TRP ILE ASN MET LEU ASP ILE SER SEQRES 25 A 389 TYR THR LEU ALA GLU VAL THR LEU GLU GLU ALA MET GLU SEQRES 26 A 389 ALA VAL VAL GLU VAL ALA ARG SER ASP GLY LEU VAL ILE SEQRES 27 A 389 GLY PRO SER GLY GLY ALA ALA VAL LYS ALA LEU ALA LYS SEQRES 28 A 389 LYS ALA ALA GLU GLY ASP LEU GLU PRO GLY ASP TYR VAL SEQRES 29 A 389 VAL VAL VAL PRO ASP THR GLY PHE LYS TYR LEU SER LEU SEQRES 30 A 389 VAL GLN ASN ALA LEU GLU GLY ALA GLY ASP SER VAL SEQRES 1 B 389 MET ALA LEU ALA ASP ILE SER GLY TYR LEU ASP VAL LEU SEQRES 2 B 389 ASP SER VAL ARG GLY PHE SER TYR LEU GLU ASN ALA ARG SEQRES 3 B 389 GLU VAL LEU ARG SER GLY GLU ALA ARG CYS LEU GLY ASN SEQRES 4 B 389 PRO ARG SER GLU PRO GLU TYR VAL LYS ALA LEU TYR VAL SEQRES 5 B 389 ILE GLY ALA SER ARG ILE PRO VAL GLY ASP GLY CYS SER SEQRES 6 B 389 HIS THR LEU GLU GLU LEU GLY VAL PHE ASP ILE SER VAL SEQRES 7 B 389 PRO GLY GLU MET VAL PHE PRO SER PRO LEU ASP PHE PHE SEQRES 8 B 389 GLU ARG GLY LYS PRO THR PRO LEU VAL ARG SER ARG LEU SEQRES 9 B 389 GLN LEU PRO ASN GLY VAL ARG VAL TRP LEU LYS LEU GLU SEQRES 10 B 389 TRP TYR ASN PRO PHE SER LEU SER VAL ALA ASP ARG PRO SEQRES 11 B 389 ALA VAL GLU ILE ILE SER ARG LEU SER ARG ARG VAL GLU SEQRES 12 B 389 LYS GLY SER LEU VAL ALA ASP ALA THR SER SER ASN PHE SEQRES 13 B 389 GLY VAL ALA LEU SER ALA VAL ALA ARG LEU TYR GLY TYR SEQRES 14 B 389 ARG ALA ARG VAL TYR LEU PRO GLY ALA ALA GLU GLU PHE SEQRES 15 B 389 GLY LYS LEU LEU PRO ARG LEU LEU GLY ALA GLN VAL ILE SEQRES 16 B 389 VAL ASP PRO GLU ALA PRO SER THR VAL HIS LEU LEU PRO SEQRES 17 B 389 ARG VAL MET LYS ASP SER LYS ASN GLU GLY PHE VAL HIS SEQRES 18 B 389 VAL ASN GLN PHE TYR ASN ASP ALA ASN PHE GLU ALA HIS SEQRES 19 B 389 MET ARG GLY THR ALA ARG GLU ILE PHE VAL GLN SER ARG SEQRES 20 B 389 ARG GLY GLY LEU ALA LEU ARG GLY VAL ALA GLY SER LEU SEQRES 21 B 389 GLY THR SER GLY HIS MET SER ALA ALA ALA PHE TYR LEU SEQRES 22 B 389 GLN SER VAL ASP PRO SER ILE ARG ALA VAL LEU VAL GLN SEQRES 23 B 389 PRO ALA GLN GLY ASP SER ILE PRO GLY ILE ARG ARG VAL SEQRES 24 B 389 GLU THR GLY MET LEU TRP ILE ASN MET LEU ASP ILE SER SEQRES 25 B 389 TYR THR LEU ALA GLU VAL THR LEU GLU GLU ALA MET GLU SEQRES 26 B 389 ALA VAL VAL GLU VAL ALA ARG SER ASP GLY LEU VAL ILE SEQRES 27 B 389 GLY PRO SER GLY GLY ALA ALA VAL LYS ALA LEU ALA LYS SEQRES 28 B 389 LYS ALA ALA GLU GLY ASP LEU GLU PRO GLY ASP TYR VAL SEQRES 29 B 389 VAL VAL VAL PRO ASP THR GLY PHE LYS TYR LEU SER LEU SEQRES 30 B 389 VAL GLN ASN ALA LEU GLU GLY ALA GLY ASP SER VAL HET PLP A 401 15 HET OAS A 402 10 HET MPD A 403 8 HET PLP B 401 15 HET OAS B 402 10 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM OAS O-ACETYLSERINE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 3 PLP 2(C8 H10 N O6 P) FORMUL 4 OAS 2(C5 H9 N O4) FORMUL 5 MPD C6 H14 O2 FORMUL 8 HOH *99(H2 O) HELIX 1 1 SER A 7 TYR A 9 5 3 HELIX 2 2 LEU A 10 VAL A 16 1 7 HELIX 3 3 TYR A 21 GLY A 32 1 12 HELIX 4 4 ASN A 39 SER A 42 5 4 HELIX 5 5 GLU A 43 GLY A 54 1 12 HELIX 6 6 SER A 86 GLY A 94 1 9 HELIX 7 7 LEU A 106 ASN A 108 5 3 HELIX 8 8 TRP A 118 ASN A 120 5 3 HELIX 9 9 ALA A 127 VAL A 142 1 16 HELIX 10 10 SER A 154 TYR A 167 1 14 HELIX 11 11 GLU A 181 GLY A 191 1 11 HELIX 12 12 THR A 203 HIS A 205 5 3 HELIX 13 13 LEU A 206 GLY A 218 1 13 HELIX 14 14 ASN A 227 GLY A 237 1 11 HELIX 15 15 GLY A 237 GLY A 249 1 13 HELIX 16 16 SER A 263 ASP A 277 1 15 HELIX 17 17 ARG A 298 GLY A 302 5 5 HELIX 18 18 MET A 303 LEU A 309 1 7 HELIX 19 19 THR A 319 GLY A 335 1 17 HELIX 20 20 GLY A 339 GLY A 356 1 18 HELIX 21 21 THR A 370 LYS A 373 5 4 HELIX 22 22 TYR A 374 LEU A 382 1 9 HELIX 23 23 SER B 7 LEU B 10 5 4 HELIX 24 24 ASP B 11 VAL B 16 1 6 HELIX 25 25 TYR B 21 GLY B 32 1 12 HELIX 26 26 ASN B 39 SER B 42 5 4 HELIX 27 27 GLU B 43 ILE B 53 1 11 HELIX 28 28 LEU B 68 GLY B 72 1 5 HELIX 29 29 SER B 86 GLY B 94 1 9 HELIX 30 30 TRP B 118 ASN B 120 5 3 HELIX 31 31 ALA B 127 ARG B 140 1 14 HELIX 32 32 SER B 154 TYR B 167 1 14 HELIX 33 33 GLU B 180 GLY B 191 1 12 HELIX 34 34 THR B 203 HIS B 205 5 3 HELIX 35 35 LEU B 206 GLY B 218 1 13 HELIX 36 36 ASN B 227 GLY B 237 1 11 HELIX 37 37 GLY B 237 GLY B 249 1 13 HELIX 38 38 SER B 263 ASP B 277 1 15 HELIX 39 39 MET B 303 LEU B 309 1 7 HELIX 40 40 THR B 319 GLY B 335 1 17 HELIX 41 41 GLY B 339 GLY B 356 1 18 HELIX 42 42 THR B 370 LYS B 373 5 4 HELIX 43 43 TYR B 374 LEU B 382 1 9 SHEET 1 A 2 LEU A 3 ASP A 5 0 SHEET 2 A 2 ARG A 57 PRO A 59 -1 O ILE A 58 N ALA A 4 SHEET 1 B 2 GLU A 33 ARG A 35 0 SHEET 2 B 2 SER A 65 THR A 67 -1 O HIS A 66 N ALA A 34 SHEET 1 C 7 VAL A 83 PHE A 84 0 SHEET 2 C 7 LEU B 99 ARG B 101 1 O LEU B 99 N PHE A 84 SHEET 3 C 7 VAL B 110 LEU B 116 -1 O LEU B 114 N VAL B 100 SHEET 4 C 7 GLY B 361 VAL B 367 1 O TYR B 363 N ARG B 111 SHEET 5 C 7 LEU B 253 GLY B 258 1 N ARG B 254 O ASP B 362 SHEET 6 C 7 ARG B 281 PRO B 287 1 O VAL B 283 N VAL B 256 SHEET 7 C 7 THR B 314 VAL B 318 1 O ALA B 316 N GLN B 286 SHEET 1 D 7 THR A 314 VAL A 318 0 SHEET 2 D 7 ARG A 281 PRO A 287 1 N LEU A 284 O THR A 314 SHEET 3 D 7 LEU A 253 GLY A 258 1 N VAL A 256 O VAL A 283 SHEET 4 D 7 GLY A 361 VAL A 367 1 O VAL A 366 N ALA A 257 SHEET 5 D 7 VAL A 110 LEU A 116 1 N ARG A 111 O GLY A 361 SHEET 6 D 7 LEU A 99 ARG A 101 -1 N VAL A 100 O LEU A 114 SHEET 7 D 7 VAL B 83 PHE B 84 1 O PHE B 84 N LEU A 99 SHEET 1 E 4 GLN A 193 ASP A 197 0 SHEET 2 E 4 ARG A 170 PRO A 176 1 N LEU A 175 O ASP A 197 SHEET 3 E 4 LEU A 147 ALA A 151 1 N ASP A 150 O TYR A 174 SHEET 4 E 4 VAL A 220 HIS A 221 1 O VAL A 220 N LEU A 147 SHEET 1 F 2 LEU B 3 ASP B 5 0 SHEET 2 F 2 ARG B 57 PRO B 59 -1 O ILE B 58 N ALA B 4 SHEET 1 G 2 GLU B 33 ARG B 35 0 SHEET 2 G 2 SER B 65 THR B 67 -1 O HIS B 66 N ALA B 34 SHEET 1 H 4 GLN B 193 ASP B 197 0 SHEET 2 H 4 ARG B 170 PRO B 176 1 N LEU B 175 O ILE B 195 SHEET 3 H 4 LEU B 147 ALA B 151 1 N VAL B 148 O ARG B 170 SHEET 4 H 4 VAL B 220 HIS B 221 1 O VAL B 220 N LEU B 147 SSBOND 1 CYS A 36 CYS A 64 1555 1555 2.08 SSBOND 2 CYS B 36 CYS B 64 1555 1555 2.07 LINK C4A PLP A 401 N OAS A 402 1555 1555 1.74 LINK C4A PLP B 401 N OAS B 402 1555 1555 1.79 CISPEP 1 LYS A 95 PRO A 96 0 -3.48 CISPEP 2 LYS B 95 PRO B 96 0 4.00 CISPEP 3 GLU B 383 GLY B 384 0 21.44 SITE 1 AC1 17 ASN A 155 LEU A 260 GLY A 261 THR A 262 SITE 2 AC1 17 SER A 263 GLY A 264 HIS A 265 GLY A 295 SITE 3 AC1 17 ILE A 296 SER A 341 PRO A 368 ASP A 369 SITE 4 AC1 17 TYR A 374 OAS A 402 HOH A 506 HOH A 529 SITE 5 AC1 17 HOH A 535 SITE 1 AC2 14 THR A 152 SER A 153 SER A 154 ASN A 155 SITE 2 AC2 14 PHE A 156 THR A 203 GLN A 224 PHE A 225 SITE 3 AC2 14 GLY A 261 THR A 262 GLY A 295 PLP A 401 SITE 4 AC2 14 HOH A 506 HOH A 511 SITE 1 AC3 7 MET A 82 GLY A 94 PRO A 96 THR A 97 SITE 2 AC3 7 TYR A 119 MET B 82 TYR B 119 SITE 1 AC4 18 ASN B 155 SER B 259 GLY B 261 THR B 262 SITE 2 AC4 18 SER B 263 GLY B 264 HIS B 265 PRO B 294 SITE 3 AC4 18 GLY B 295 ILE B 296 SER B 341 PRO B 368 SITE 4 AC4 18 TYR B 374 OAS B 402 HOH B 501 HOH B 519 SITE 5 AC4 18 HOH B 530 HOH B 536 SITE 1 AC5 11 THR B 152 SER B 153 ASN B 155 PHE B 156 SITE 2 AC5 11 GLN B 224 PHE B 225 GLY B 261 THR B 262 SITE 3 AC5 11 GLY B 295 ARG B 297 PLP B 401 CRYST1 75.646 75.646 275.784 90.00 90.00 90.00 P 43 21 2 16 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 0.013219 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013219 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003626 0.00000