HEADER LYASE 07-JUL-11 3SS7 TITLE CRYSTAL STRUCTURE OF HOLO D-SERINE DEHYDRATASE FROM ESCHERICHIA COLI TITLE 2 AT 1.55 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-SERINE DEHYDRATASE; COMPND 3 CHAIN: X; COMPND 4 SYNONYM: D-SERINE DEAMINASE, DSD; COMPND 5 EC: 4.3.1.18; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: B2366, DSDA, DSDA B2366JW2393, JW2363; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS D-SERINE DEHYDRATASE, TYPE II FOLD, ALFA,BETA-ELIMINATION, PYRIDOXAL- KEYWDS 2 5'-PHOSPHATE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR D.V.URUSOVA,M.N.ISUPOV,S.V.ANTONYUK,G.S.KACHALOVA,A.A.VAGIN, AUTHOR 2 A.A.LEBEDEV,G.P.BOURENKOV,Z.DAUTER,H.D.BARTUNIK,W.R.MELIK-ADAMYAN, AUTHOR 3 T.D.MUELLER,K.D.SCHNACKERZ REVDAT 2 08-FEB-12 3SS7 1 JRNL REVDAT 1 18-JAN-12 3SS7 0 JRNL AUTH D.V.URUSOVA,M.N.ISUPOV,S.ANTONYUK,G.S.KACHALOVA,G.OBLOMOVA, JRNL AUTH 2 A.A.VAGIN,A.A.LEBEDEV,G.P.BOURENKO,Z.DAUTER,H.D.BARTUNIK, JRNL AUTH 3 V.S.LAMZIN,W.R.MELIK-ADAMYAN,T.D.MUELLER,K.D.SCHNACKERZ JRNL TITL CRYSTAL STRUCTURE OF D-SERINE DEHYDRATASE FROM ESCHERICHIA JRNL TITL 2 COLI. JRNL REF BIOCHIM.BIOPHYS.ACTA V.1824 422 2011 JRNL REFN ISSN 0006-3002 JRNL PMID 22197591 JRNL DOI 10.1016/J.BBAPAP.2011.10.017 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 70687 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) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3546 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) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3994 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 77.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.2700 REMARK 3 BIN FREE R VALUE SET COUNT : 214 REMARK 3 BIN FREE R VALUE : 0.3330 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3324 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 668 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.36000 REMARK 3 B22 (A**2) : 0.25000 REMARK 3 B33 (A**2) : 0.21000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.19000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.077 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.049 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.307 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3552 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4846 ; 1.524 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 479 ; 5.351 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 157 ;36.805 ;24.395 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 595 ;12.761 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;14.080 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 535 ; 0.106 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2733 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1939 ; 0.240 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2492 ; 0.313 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 585 ; 0.159 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 3 ; 0.378 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 53 ; 0.218 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 56 ; 0.217 ; 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): 2228 ; 0.900 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3578 ; 1.503 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1340 ; 2.466 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1246 ; 3.765 ; 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 3SS7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUL-11. REMARK 100 THE RCSB ID CODE IS RCSB066586. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX10.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 73947 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 72.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08500 REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.41000 REMARK 200 FOR SHELL : 2.250 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.7 M SODIUM CITRATE, 0.1 M IMIDAZOLE/ REMARK 280 MALEATE BUFFER, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 23.90300 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: X 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 X 1 REMARK 465 GLU X 2 REMARK 465 ASN X 3 REMARK 465 ALA X 4 REMARK 465 LYS X 5 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 GLU X 221 CD OE1 OE2 REMARK 470 LYS X 225 CD CE NZ 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 OG1 THR X 141 OD1 ASP X 143 2.14 REMARK 500 OE1 GLN X 404 O HOH X 716 2.18 REMARK 500 N MET X 6 O HOH X 848 2.19 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 OG SER X 8 O HOH X 846 2545 2.10 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 VAL X 186 CB - CA - C ANGL. DEV. = -14.0 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 X 113 -53.74 76.35 REMARK 500 ARG X 120 -76.60 -86.30 REMARK 500 SER X 309 55.79 -147.51 REMARK 500 HIS X 321 -127.97 51.64 REMARK 500 SER X 346 153.40 -42.79 REMARK 500 PHE X 348 -21.82 -146.72 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 K X 503 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU X 305 OE1 REMARK 620 2 GLY X 279 O 125.4 REMARK 620 3 CYS X 278 O 106.3 87.1 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL X 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP X 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K X 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3SS9 RELATED DB: PDB REMARK 900 RELATED ID: 3GWQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A PUTATIVE D-SERINE DEAMINASE (BXE_ REMARK 900 A4060) FROM BURKHOLDERIA XENOVORANS LB400 AT 2.00 A REMARK 900 RESOLUTION REMARK 900 RELATED ID: 3AWO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF D-SERINE DEHYDRATASE IN COMPLEX WITH D REMARK 900 -SERINE FROM CHICKEN KIDNEY (EDTA-TREATED REMARK 900 RELATED ID: 3AWN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF D-SERINE DEHYDRATASE FROM CHICKEN REMARK 900 KIDNEY (EDTA TREATED) REMARK 900 RELATED ID: 3ANV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF D-SERINE DEHYDRATASE FROM CHICKEN REMARK 900 KIDNEY (2,3-DAP COMPLEX) REMARK 900 RELATED ID: 3ANU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF D-SERINE DEHYDRATASE FROM CHICKEN REMARK 900 KIDNEY REMARK 900 RELATED ID: 3ROZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF APO D-SERINE DEAMINASE FROM SALMONELLA REMARK 900 TYPHIMURIUM DBREF 3SS7 X 1 442 UNP P00926 SDHD_ECOLI 1 442 SEQRES 1 X 442 MET GLU ASN ALA LYS MET ASN SER LEU ILE ALA GLN TYR SEQRES 2 X 442 PRO LEU VAL LYS ASP LEU VAL ALA LEU LYS GLU THR THR SEQRES 3 X 442 TRP PHE ASN PRO GLY THR THR SER LEU ALA GLU GLY LEU SEQRES 4 X 442 PRO TYR VAL GLY LEU THR GLU GLN ASP VAL GLN ASP ALA SEQRES 5 X 442 HIS ALA ARG LEU SER ARG PHE ALA PRO TYR LEU ALA LYS SEQRES 6 X 442 ALA PHE PRO GLU THR ALA ALA THR GLY GLY ILE ILE GLU SEQRES 7 X 442 SER GLU LEU VAL ALA ILE PRO ALA MET GLN LYS ARG LEU SEQRES 8 X 442 GLU LYS GLU TYR GLN GLN PRO ILE SER GLY GLN LEU LEU SEQRES 9 X 442 LEU LYS LYS ASP SER HIS LEU PRO ILE SER GLY SER ILE SEQRES 10 X 442 LYS ALA ARG GLY GLY ILE TYR GLU VAL LEU ALA HIS ALA SEQRES 11 X 442 GLU LYS LEU ALA LEU GLU ALA GLY LEU LEU THR LEU ASP SEQRES 12 X 442 ASP ASP TYR SER LYS LEU LEU SER PRO GLU PHE LYS GLN SEQRES 13 X 442 PHE PHE SER GLN TYR SER ILE ALA VAL GLY SER THR GLY SEQRES 14 X 442 ASN LEU GLY LEU SER ILE GLY ILE MET SER ALA ARG ILE SEQRES 15 X 442 GLY PHE LYS VAL THR VAL HIS MET SER ALA ASP ALA ARG SEQRES 16 X 442 ALA TRP LYS LYS ALA LYS LEU ARG SER HIS GLY VAL THR SEQRES 17 X 442 VAL VAL GLU TYR GLU GLN ASP TYR GLY VAL ALA VAL GLU SEQRES 18 X 442 GLU GLY ARG LYS ALA ALA GLN SER ASP PRO ASN CYS PHE SEQRES 19 X 442 PHE ILE ASP ASP GLU ASN SER ARG THR LEU PHE LEU GLY SEQRES 20 X 442 TYR SER VAL ALA GLY GLN ARG LEU LYS ALA GLN PHE ALA SEQRES 21 X 442 GLN GLN GLY ARG ILE VAL ASP ALA ASP ASN PRO LEU PHE SEQRES 22 X 442 VAL TYR LEU PRO CYS GLY VAL GLY GLY GLY PRO GLY GLY SEQRES 23 X 442 VAL ALA PHE GLY LEU LYS LEU ALA PHE GLY ASP HIS VAL SEQRES 24 X 442 HIS CYS PHE PHE ALA GLU PRO THR HIS SER PRO CYS MET SEQRES 25 X 442 LEU LEU GLY VAL HIS THR GLY LEU HIS ASP GLN ILE SER SEQRES 26 X 442 VAL GLN ASP ILE GLY ILE ASP ASN LEU THR ALA ALA ASP SEQRES 27 X 442 GLY LEU ALA VAL GLY ARG ALA SER GLY PHE VAL GLY ARG SEQRES 28 X 442 ALA MET GLU ARG LEU LEU ASP GLY PHE TYR THR LEU SER SEQRES 29 X 442 ASP GLN THR MET TYR ASP MET LEU GLY TRP LEU ALA GLN SEQRES 30 X 442 GLU GLU GLY ILE ARG LEU GLU PRO SER ALA LEU ALA GLY SEQRES 31 X 442 MET ALA GLY PRO GLN ARG VAL CYS ALA SER VAL SER TYR SEQRES 32 X 442 GLN GLN MET HIS GLY PHE SER ALA GLU GLN LEU ARG ASN SEQRES 33 X 442 THR THR HIS LEU VAL TRP ALA THR GLY GLY GLY MET VAL SEQRES 34 X 442 PRO GLU GLU GLU MET ASN GLN TYR LEU ALA LYS GLY ARG HET GOL X 501 6 HET PLP X 502 15 HET K X 503 1 HETNAM GOL GLYCEROL HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM K POTASSIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 2 GOL C3 H8 O3 FORMUL 3 PLP C8 H10 N O6 P FORMUL 4 K K 1+ FORMUL 5 HOH *668(H2 O) HELIX 1 1 MET X 6 TYR X 13 1 8 HELIX 2 2 PRO X 14 ALA X 21 1 8 HELIX 3 3 SER X 34 LEU X 39 1 6 HELIX 4 4 PRO X 40 VAL X 42 5 3 HELIX 5 5 THR X 45 PHE X 67 1 23 HELIX 6 6 PRO X 68 GLY X 74 5 7 HELIX 7 7 ILE X 84 GLN X 96 1 13 HELIX 8 8 SER X 109 LEU X 111 5 3 HELIX 9 9 ILE X 117 ALA X 137 1 21 HELIX 10 10 ASP X 145 LEU X 150 5 6 HELIX 11 11 SER X 151 GLN X 160 1 10 HELIX 12 12 GLY X 169 GLY X 183 1 15 HELIX 13 13 ARG X 195 HIS X 205 1 11 HELIX 14 14 ASP X 215 SER X 229 1 15 HELIX 15 15 SER X 241 VAL X 250 1 10 HELIX 16 16 VAL X 250 GLY X 263 1 14 HELIX 17 17 GLY X 281 GLY X 296 1 16 HELIX 18 18 PRO X 310 GLY X 319 1 10 HELIX 19 19 LEU X 320 ILE X 324 5 5 HELIX 20 20 SER X 325 GLY X 330 5 6 HELIX 21 21 ALA X 337 ALA X 341 5 5 HELIX 22 22 PHE X 348 GLU X 354 1 7 HELIX 23 23 ARG X 355 LEU X 357 5 3 HELIX 24 24 SER X 364 GLY X 380 1 17 HELIX 25 25 GLU X 384 MET X 391 5 8 HELIX 26 26 ALA X 392 SER X 400 1 9 HELIX 27 27 SER X 400 GLY X 408 1 9 HELIX 28 28 SER X 410 ASN X 416 1 7 HELIX 29 29 PRO X 430 GLY X 441 1 12 SHEET 1 A 7 THR X 26 PHE X 28 0 SHEET 2 A 7 GLY X 359 LEU X 363 -1 O PHE X 360 N TRP X 27 SHEET 3 A 7 VAL X 299 PRO X 306 1 N PHE X 303 O TYR X 361 SHEET 4 A 7 LEU X 272 PRO X 277 1 N LEU X 276 O PHE X 302 SHEET 5 A 7 THR X 418 ALA X 423 1 O LEU X 420 N PHE X 273 SHEET 6 A 7 GLN X 102 LYS X 107 1 N LEU X 104 O HIS X 419 SHEET 7 A 7 LEU X 81 ALA X 83 -1 N VAL X 82 O LEU X 105 SHEET 1 B 4 THR X 208 TYR X 212 0 SHEET 2 B 4 LYS X 185 SER X 191 1 N MET X 190 O VAL X 210 SHEET 3 B 4 SER X 162 GLY X 166 1 N VAL X 165 O HIS X 189 SHEET 4 B 4 CYS X 233 PHE X 235 1 O PHE X 234 N SER X 162 LINK OE1 GLU X 305 K K X 503 1555 1555 2.28 LINK O GLY X 279 K K X 503 1555 1555 2.41 LINK O CYS X 278 K K X 503 1555 1555 2.65 LINK NZ LYS X 118 C4A PLP X 502 1555 1555 1.32 SITE 1 AC1 5 ALA X 392 ARG X 396 HOH X 699 HOH X 943 SITE 2 AC1 5 HOH X1030 SITE 1 AC2 15 LYS X 118 ASN X 170 GLY X 279 VAL X 280 SITE 2 AC2 15 GLY X 281 GLY X 282 GLY X 283 PRO X 284 SITE 3 AC2 15 LEU X 340 GLU X 384 THR X 424 HOH X 781 SITE 4 AC2 15 HOH X 884 HOH X 993 HOH X 997 SITE 1 AC3 6 CYS X 278 GLY X 279 GLU X 305 SER X 309 SITE 2 AC3 6 CYS X 311 HOH X 854 CRYST1 73.774 47.806 75.193 90.00 104.96 90.00 P 1 21 1 2 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 0.013555 0.000000 0.003622 0.00000 SCALE2 0.000000 0.020918 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013766 0.00000