HEADER TRANSFERASE 15-NOV-07 2VGV TITLE CRYSTAL STRUCTURE OF E53QBSSHMT OBTAINED IN THE PRESENCE OF L-ALLO- TITLE 2 THREONINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE HYDROXYMETHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-405; COMPND 5 EC: 2.1.2.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1422; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PRSET C KEYWDS PLP-DEPENDENT ENZYMES, SHMT, E53Q, TRANSFERASE, ENZYME MEMORY, KEYWDS 2 PYRIDOXAL PHOSPHATE, ONE-CARBON METABOLISM EXPDTA X-RAY DIFFRACTION AUTHOR V.RAJARAM,B.S.BHAVANI,P.KAUL,V.PRAKASH,N.APPAJI RAO,H.S.SAVITHRI, AUTHOR 2 M.R.N.MURTHY REVDAT 4 13-DEC-23 2VGV 1 LINK REVDAT 3 24-FEB-09 2VGV 1 VERSN REVDAT 2 11-DEC-07 2VGV 1 AUTHOR REVDAT 1 04-DEC-07 2VGV 0 JRNL AUTH V.RAJARAM,B.S.BHAVANI,P.KAUL,V.PRAKASH,N.APPAJI RAO, JRNL AUTH 2 H.S.SAVITHRI,M.R.N.MURTHY JRNL TITL STRUCTURE DETERMINATION AND BIOCHEMICAL STUDIES ON BACILLUS JRNL TITL 2 STEAROTHERMOPHILUS E53Q SERINE HYDROXYMETHYLTRANSFERASE AND JRNL TITL 3 ITS COMPLEXES PROVIDE INSIGHTS ON FUNCTION AND ENZYME MEMORY JRNL REF FEBS J. V. 274 4148 2007 JRNL REFN ISSN 1742-464X JRNL PMID 17651438 JRNL DOI 10.1111/J.1742-4658.2007.05943.X REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 14641 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1619 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 998 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2150 REMARK 3 BIN FREE R VALUE SET COUNT : 111 REMARK 3 BIN FREE R VALUE : 0.3140 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3117 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 219 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.07000 REMARK 3 B33 (A**2) : -0.07000 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): 0.765 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.276 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.170 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.858 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.899 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3212 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4355 ; 1.009 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 404 ; 5.141 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 149 ;36.094 ;24.094 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 522 ;13.522 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;15.258 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 482 ; 0.066 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2475 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1560 ; 0.176 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2231 ; 0.294 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 222 ; 0.105 ; 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): 87 ; 0.137 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 29 ; 0.148 ; 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): 2085 ; 0.287 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3230 ; 0.503 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1262 ; 0.752 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1125 ; 1.268 ; 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2VGV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-NOV-07. REMARK 100 THE DEPOSITION ID IS D_1290034432. 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 : 7.5 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : OSMIC MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16978 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL 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) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.36000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1KL1 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% MPD, 0.1 M HEPES, PH 7.5, 0.2 MM REMARK 280 EDTA, 5 MM 2-MERCAPTOETHANOL, 10 MM L-ALLO-THREONINE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 30.56350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.10250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.56350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.10250 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: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 8710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, GLU 53 TO GLN 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 GLY A 407 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 GLY A 406 CA C O 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 HIS A 125 34.68 -98.18 REMARK 500 ALA A 170 165.72 104.51 REMARK 500 ALA A 173 51.38 -146.20 REMARK 500 HIS A 225 -160.02 -75.48 REMARK 500 LYS A 226 -137.35 68.68 REMARK 500 ASN A 310 -137.66 -127.38 REMARK 500 THR A 353 162.72 68.63 REMARK 500 ASP A 405 150.34 76.16 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 A1407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLY A1408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A1409 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YJZ RELATED DB: PDB REMARK 900 K226M MUTANT OF SERINE HYDROXYMETHYLTRANSFERASE FROM REMARK 900 B.STEAROTHERMOPHILUS REMARK 900 RELATED ID: 1YJY RELATED DB: PDB REMARK 900 K226M MUTANT OF SERINE HYDROXYMETHYLTRANSFERASE FROM REMARK 900 B.STEAROTHERMOPHILUS, COMPLEX WITH SERINE REMARK 900 RELATED ID: 1KKJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASE REMARK 900 FROMB.STEAROTHERMOPHILUS REMARK 900 RELATED ID: 1YJS RELATED DB: PDB REMARK 900 K226Q MUTANT OF SERINE HYDROXYMETHYLTRANSFERASE FROM REMARK 900 B.STEAROTHERMOPHILUS, COMPLEX WITH GLYCINE REMARK 900 RELATED ID: 1KL2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASECOMPLEXED WITH REMARK 900 GLYCINE AND 5-FORMYL TETRAHYDROFOLATE REMARK 900 RELATED ID: 1KL1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASECOMPLEXED WITH REMARK 900 GLYCINE REMARK 900 RELATED ID: 1KKP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASECOMPLEXED WITH REMARK 900 SERINE REMARK 900 RELATED ID: 2VGS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E53QBSSHMT INTERNAL ALDIMINE REMARK 900 RELATED ID: 2VGT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E53QBSSHMT WITH GLYCINE REMARK 900 RELATED ID: 2VGU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E53QBSSHMT WITH L- SERINE REMARK 900 RELATED ID: 2VGW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E53QBSSHMT OBTAINED IN THE PRESENCE OF GLYCINE REMARK 900 AND 5-FOMYL TETRAHYDROFOLATE DBREF 2VGV A 1 405 UNP Q7SIB6 Q7SIB6_BACST 1 405 DBREF 2VGV A 406 407 PDB 2VGV 2VGV 406 407 SEQADV 2VGV GLN A 53 UNP Q7SIB6 GLU 53 ENGINEERED MUTATION SEQRES 1 A 407 MET LYS TYR LEU PRO GLN GLN ASP PRO GLN VAL PHE ALA SEQRES 2 A 407 ALA ILE GLU GLN GLU ARG LYS ARG GLN HIS ALA LYS ILE SEQRES 3 A 407 GLU LEU ILE ALA SER GLU ASN PHE VAL SER ARG ALA VAL SEQRES 4 A 407 MET GLU ALA GLN GLY SER VAL LEU THR ASN LYS TYR ALA SEQRES 5 A 407 GLN GLY TYR PRO GLY ARG ARG TYR TYR GLY GLY CYS GLU SEQRES 6 A 407 TYR VAL ASP ILE VAL GLU GLU LEU ALA ARG GLU ARG ALA SEQRES 7 A 407 LYS GLN LEU PHE GLY ALA GLU HIS ALA ASN VAL GLN PRO SEQRES 8 A 407 HIS SER GLY ALA GLN ALA ASN MET ALA VAL TYR PHE THR SEQRES 9 A 407 VAL LEU GLU HIS GLY ASP THR VAL LEU GLY MET ASN LEU SEQRES 10 A 407 SER HIS GLY GLY HIS LEU THR HIS GLY SER PRO VAL ASN SEQRES 11 A 407 PHE SER GLY VAL GLN TYR ASN PHE VAL ALA TYR GLY VAL SEQRES 12 A 407 ASP PRO GLU THR HIS VAL ILE ASP TYR ASP ASP VAL ARG SEQRES 13 A 407 GLU LYS ALA ARG LEU HIS ARG PRO LYS LEU ILE VAL ALA SEQRES 14 A 407 ALA ALA SER ALA TYR PRO ARG ILE ILE ASP PHE ALA LYS SEQRES 15 A 407 PHE ARG GLU ILE ALA ASP GLU VAL GLY ALA TYR LEU MET SEQRES 16 A 407 VAL ASP MET ALA HIS ILE ALA GLY LEU VAL ALA ALA GLY SEQRES 17 A 407 LEU HIS PRO ASN PRO VAL PRO TYR ALA HIS PHE VAL THR SEQRES 18 A 407 THR THR THR HIS LYS THR LEU ARG GLY PRO ARG GLY GLY SEQRES 19 A 407 MET ILE LEU CYS GLN GLU GLN PHE ALA LYS GLN ILE ASP SEQRES 20 A 407 LYS ALA ILE PHE PRO GLY ILE GLN GLY GLY PRO LEU MET SEQRES 21 A 407 HIS VAL ILE ALA ALA LYS ALA VAL ALA PHE GLY GLU ALA SEQRES 22 A 407 LEU GLN ASP ASP PHE LYS ALA TYR ALA LYS ARG VAL VAL SEQRES 23 A 407 ASP ASN ALA LYS ARG LEU ALA SER ALA LEU GLN ASN GLU SEQRES 24 A 407 GLY PHE THR LEU VAL SER GLY GLY THR ASP ASN HIS LEU SEQRES 25 A 407 LEU LEU VAL ASP LEU ARG PRO GLN GLN LEU THR GLY LYS SEQRES 26 A 407 THR ALA GLU LYS VAL LEU ASP GLU VAL GLY ILE THR VAL SEQRES 27 A 407 ASN LYS ASN THR ILE PRO TYR ASP PRO GLU SER PRO PHE SEQRES 28 A 407 VAL THR SER GLY ILE ARG ILE GLY THR ALA ALA VAL THR SEQRES 29 A 407 THR ARG GLY PHE GLY LEU GLU GLU MET ASP GLU ILE ALA SEQRES 30 A 407 ALA ILE ILE GLY LEU VAL LEU LYS ASN VAL GLY SER GLU SEQRES 31 A 407 GLN ALA LEU GLU GLU ALA ARG GLN ARG VAL ALA ALA LEU SEQRES 32 A 407 THR ASP GLY GLY HET GLY A1408 10 HET PLP A1407 15 HET MPD A1409 8 HETNAM GLY GLYCINE HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 2 GLY C2 H5 N O2 FORMUL 3 PLP C8 H10 N O6 P FORMUL 4 MPD C6 H14 O2 FORMUL 5 HOH *219(H2 O) HELIX 1 1 TYR A 3 ASP A 8 1 6 HELIX 2 2 ASP A 8 LYS A 25 1 18 HELIX 3 3 SER A 36 GLY A 44 1 9 HELIX 4 4 SER A 45 LYS A 50 5 6 HELIX 5 5 CYS A 64 GLY A 83 1 20 HELIX 6 6 SER A 93 LEU A 106 1 14 HELIX 7 7 LEU A 117 GLY A 120 5 4 HELIX 8 8 HIS A 122 GLY A 126 5 5 HELIX 9 9 ASN A 130 TYR A 136 1 7 HELIX 10 10 ASP A 151 ARG A 163 1 13 HELIX 11 11 ASP A 179 GLY A 191 1 13 HELIX 12 12 ILE A 201 ALA A 207 1 7 HELIX 13 13 HIS A 225 ARG A 229 5 5 HELIX 14 14 PHE A 242 PHE A 251 1 10 HELIX 15 15 LEU A 259 GLN A 275 1 17 HELIX 16 16 GLN A 275 GLY A 300 1 26 HELIX 17 17 SER A 305 GLY A 307 5 3 HELIX 18 18 ARG A 318 GLN A 321 5 4 HELIX 19 19 THR A 323 VAL A 334 1 12 HELIX 20 20 THR A 360 ARG A 366 1 7 HELIX 21 21 GLY A 369 LYS A 385 1 17 HELIX 22 22 SER A 389 THR A 404 1 16 SHEET 1 AA 2 ILE A 26 GLU A 27 0 SHEET 2 AA 2 ILE A 336 THR A 337 1 N THR A 337 O ILE A 26 SHEET 1 AB 2 GLY A 54 TYR A 55 0 SHEET 2 AB 2 ARG A 58 ARG A 59 -1 O ARG A 58 N TYR A 55 SHEET 1 AC 7 HIS A 86 ASN A 88 0 SHEET 2 AC 7 GLY A 234 CYS A 238 -1 O ILE A 236 N ASN A 88 SHEET 3 AC 7 PHE A 219 THR A 223 -1 O VAL A 220 N LEU A 237 SHEET 4 AC 7 TYR A 193 ASP A 197 1 O LEU A 194 N PHE A 219 SHEET 5 AC 7 LEU A 166 ALA A 169 1 O ILE A 167 N MET A 195 SHEET 6 AC 7 THR A 111 MET A 115 1 O LEU A 113 N VAL A 168 SHEET 7 AC 7 ASN A 137 TYR A 141 1 O ASN A 137 N VAL A 112 SHEET 1 AD 4 THR A 302 LEU A 303 0 SHEET 2 AD 4 LEU A 312 ASP A 316 -1 O ASP A 316 N THR A 302 SHEET 3 AD 4 GLY A 355 GLY A 359 -1 O ILE A 356 N VAL A 315 SHEET 4 AD 4 ASN A 339 ASN A 341 -1 O ASN A 339 N ARG A 357 LINK C4A PLP A1407 N AGLY A1408 1555 1555 1.23 LINK C4A PLP A1407 N BGLY A1408 1555 1555 1.23 CISPEP 1 PHE A 251 PRO A 252 0 4.08 SITE 1 AC1 17 TYR A 51 SER A 93 GLY A 94 ALA A 95 SITE 2 AC1 17 HIS A 122 SER A 172 ASP A 197 ALA A 199 SITE 3 AC1 17 HIS A 200 THR A 223 HIS A 225 LYS A 226 SITE 4 AC1 17 GLY A 256 GLY A 257 GLY A1408 HOH A2218 SITE 5 AC1 17 HOH A2219 SITE 1 AC2 8 SER A 31 GLN A 53 TYR A 61 HIS A 122 SITE 2 AC2 8 HIS A 200 LYS A 226 ARG A 357 PLP A1407 SITE 1 AC3 4 TYR A 152 ARG A 156 LEU A 322 HOH A2176 CRYST1 61.127 106.205 57.065 90.00 90.00 90.00 P 21 21 2 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016359 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009416 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017524 0.00000