HEADER TRANSFERASE 29-JAN-08 2VMY TITLE CRYSTAL STRUCTURE OF F351GBSSHMT IN COMPLEX WITH GLY AND FTHF COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE HYDROXYMETHYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 1-405; COMPND 5 SYNONYM: SHMT, SERINE METHYLASE; COMPND 6 EC: 2.1.2.1; COMPND 7 ENGINEERED: YES; COMPND 8 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_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PRSET C KEYWDS TRANSFERASE, ONE-CARBON METABOLISM, PLP-DEPENDENT ENZYMES, SERINE KEYWDS 2 TERNARY COMPLEX, PYRIDOXAL PHOSPHATE, F351G, FOLATE BINDING EXPDTA X-RAY DIFFRACTION AUTHOR V.RAJARAM,V.R.PAI,S.BISHT,B.S.BHAVANI,N.APPAJI RAO,H.S.SAVITHRI, AUTHOR 2 M.R.N.MURTHY REVDAT 4 13-DEC-23 2VMY 1 REMARK LINK REVDAT 3 14-SEP-11 2VMY 1 REMARK HETNAM HETSYN VERSN REVDAT 2 30-MAR-11 2VMY 1 COMPND SOURCE KEYWDS JRNL REVDAT 2 2 1 REMARK HETNAM HETSYN FORMUL REVDAT 1 16-DEC-08 2VMY 0 JRNL AUTH V.R.PAI,V.RAJARAM,S.BISHT,B.S.BHAVANI,N.A.RAO,M.R.N.MURTHY, JRNL AUTH 2 H.S.SAVITHRI JRNL TITL STRUCTURAL AND FUNCTIONAL STUDIES OF BACILLUS JRNL TITL 2 STEAROTHERMOPHILUS SERINE HYDROXYMETHYLTRANSFERASE: THE ROLE JRNL TITL 3 OF ASN(341), TYR(60) AND PHE(351) IN TETRAHYDROFOLATE JRNL TITL 4 BINDING. JRNL REF BIOCHEM.J. V. 418 635 2009 JRNL REFN ISSN 0264-6021 JRNL PMID 19046138 JRNL DOI 10.1042/BJ20081739 REMARK 2 REMARK 2 RESOLUTION. 2.70 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 18654 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) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1007 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1370 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2980 REMARK 3 BIN FREE R VALUE SET COUNT : 68 REMARK 3 BIN FREE R VALUE : 0.3840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6218 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 116 REMARK 3 SOLVENT ATOMS : 24 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 77.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : 0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.06000 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): 0.425 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.330 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.029 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.927 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.885 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6468 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8773 ; 0.985 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 810 ; 4.669 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 297 ;35.291 ;24.141 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1044 ;15.453 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;13.051 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 966 ; 0.061 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4972 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3280 ; 0.175 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4471 ; 0.294 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 225 ; 0.126 ; 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): 31 ; 0.150 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.149 ; 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): 4169 ; 0.197 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6466 ; 0.356 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2590 ; 0.394 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2306 ; 0.679 ; 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 2VMY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-JAN-08. REMARK 100 THE DEPOSITION ID IS D_1290034690. 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 : 19879 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.51000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: PDB ENTRY 1KL2 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 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 GLY, PROTEIN INCUBATED WITH REMARK 280 2 MM FTHF 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 51.74150 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.4 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, PHE 351 TO GLY REMARK 400 ENGINEERED RESIDUE IN CHAIN B, PHE 351 TO GLY 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 ALA A 170 163.78 117.13 REMARK 500 ALA A 173 49.29 -147.57 REMARK 500 LYS A 226 -115.50 -83.00 REMARK 500 ASN A 310 -141.68 -133.53 REMARK 500 VAL A 338 -166.12 -125.34 REMARK 500 PRO A 350 7.42 -57.28 REMARK 500 VAL A 352 -60.21 -102.00 REMARK 500 THR A 353 151.45 66.91 REMARK 500 ARG B 58 65.89 -117.48 REMARK 500 ALA B 170 162.58 105.01 REMARK 500 ALA B 173 47.45 -143.33 REMARK 500 LYS B 226 -119.02 -84.87 REMARK 500 SER B 305 -5.19 80.06 REMARK 500 ASN B 310 -137.33 -133.82 REMARK 500 THR B 353 158.07 65.85 REMARK 500 ASN B 386 68.99 -110.69 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 B2004 DISTANCE = 5.88 ANGSTROMS 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLY A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FFO A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLY B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FFO B 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD B 701 REMARK 900 REMARK 900 RELATED ENTRIES 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: 2VMZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF F351GBSSHMT IN COMPLEX WITH GLY 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: 2VMV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF F351GBSSHMT INTERNAL ALDIMINE REMARK 900 RELATED ID: 2VIB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF S172ABSSHMT OBTAINED IN THE PRESENCE OF L-ALLO- REMARK 900 THR REMARK 900 RELATED ID: 2VGS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E53QBSSHMT INTERNAL ALDIMINE REMARK 900 RELATED ID: 2VMS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF Y60ABSSHMT CRYSTALLIZED IN THE PRESENCE OF REMARK 900 GLYCINE REMARK 900 RELATED ID: 1YJZ RELATED DB: PDB REMARK 900 K226M MUTANT OF SERINE HYDROXYMETHYLTRANSFERASE FROM REMARK 900 B.STEAROTHERMOPHILUS REMARK 900 RELATED ID: 2VMT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF Y60ABSSHMT L-SER EXTERNAL ALDIMINE REMARK 900 RELATED ID: 2VMN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF N341ABSSHMT INTERNAL ALDIMINE REMARK 900 RELATED ID: 2VGV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E53QBSSHMT OBTAINED IN THE PRESENCE OF L-ALLO- REMARK 900 THREONINE REMARK 900 RELATED ID: 2VMP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF N341ABSSHMT L-SER EXTERNAL ALDIMINE REMARK 900 RELATED ID: 2VMR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF Y60ABSSHMT INTERNAL ALDIMINE REMARK 900 RELATED ID: 2VGU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E53QBSSHMT WITH L-SERINE REMARK 900 RELATED ID: 2VMU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF Y60ABSSHMT CRYSTALLIZED IN THE PRESENCE OF L- REMARK 900 ALLO-THR REMARK 900 RELATED ID: 2VI9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF S172ABSSHMT GLYCINE EXTERNAL ALDIMINE 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: 2VI8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF S172ABSSHMT INTERNAL ALDIMINE 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: 2VIA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF S172ABSSHMT L-SERINE EXTERNAL ALDIMINE REMARK 900 RELATED ID: 2VMQ RELATED DB: PDB REMARK 900 STRUCTURE OF N341ABSSHMT CRYSTALLIZED IN THE PRESENCE OF L-ALLO-THR REMARK 900 RELATED ID: 2VGT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E53QBSSHMT WITH GLYCINE REMARK 900 RELATED ID: 2VMW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF F351GBSSHMT IN COMPLEX WITH L-SER REMARK 900 RELATED ID: 2VMO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF N341ABSSHMT GLY EXTERNAL ALDIMINE REMARK 900 RELATED ID: 2VMX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF F351GBSSHMT IN COMPLEX WITH L-ALLO-THR REMARK 900 RELATED ID: 1KKJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASE REMARK 900 FROMB.STEAROTHERMOPHILUS 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 2VMY A 1 405 UNP Q7SIB6 Q7SIB6_BACST 1 405 DBREF 2VMY B 1 405 UNP Q7SIB6 Q7SIB6_BACST 1 405 SEQADV 2VMY GLY A 351 UNP Q7SIB6 PHE 351 ENGINEERED MUTATION SEQADV 2VMY GLY B 351 UNP Q7SIB6 PHE 351 ENGINEERED MUTATION SEQRES 1 A 405 MET LYS TYR LEU PRO GLN GLN ASP PRO GLN VAL PHE ALA SEQRES 2 A 405 ALA ILE GLU GLN GLU ARG LYS ARG GLN HIS ALA LYS ILE SEQRES 3 A 405 GLU LEU ILE ALA SER GLU ASN PHE VAL SER ARG ALA VAL SEQRES 4 A 405 MET GLU ALA GLN GLY SER VAL LEU THR ASN LYS TYR ALA SEQRES 5 A 405 GLU GLY TYR PRO GLY ARG ARG TYR TYR GLY GLY CYS GLU SEQRES 6 A 405 TYR VAL ASP ILE VAL GLU GLU LEU ALA ARG GLU ARG ALA SEQRES 7 A 405 LYS GLN LEU PHE GLY ALA GLU HIS ALA ASN VAL GLN PRO SEQRES 8 A 405 HIS SER GLY ALA GLN ALA ASN MET ALA VAL TYR PHE THR SEQRES 9 A 405 VAL LEU GLU HIS GLY ASP THR VAL LEU GLY MET ASN LEU SEQRES 10 A 405 SER HIS GLY GLY HIS LEU THR HIS GLY SER PRO VAL ASN SEQRES 11 A 405 PHE SER GLY VAL GLN TYR ASN PHE VAL ALA TYR GLY VAL SEQRES 12 A 405 ASP PRO GLU THR HIS VAL ILE ASP TYR ASP ASP VAL ARG SEQRES 13 A 405 GLU LYS ALA ARG LEU HIS ARG PRO LYS LEU ILE VAL ALA SEQRES 14 A 405 ALA ALA SER ALA TYR PRO ARG ILE ILE ASP PHE ALA LYS SEQRES 15 A 405 PHE ARG GLU ILE ALA ASP GLU VAL GLY ALA TYR LEU MET SEQRES 16 A 405 VAL ASP MET ALA HIS ILE ALA GLY LEU VAL ALA ALA GLY SEQRES 17 A 405 LEU HIS PRO ASN PRO VAL PRO TYR ALA HIS PHE VAL THR SEQRES 18 A 405 THR THR THR HIS LYS THR LEU ARG GLY PRO ARG GLY GLY SEQRES 19 A 405 MET ILE LEU CYS GLN GLU GLN PHE ALA LYS GLN ILE ASP SEQRES 20 A 405 LYS ALA ILE PHE PRO GLY ILE GLN GLY GLY PRO LEU MET SEQRES 21 A 405 HIS VAL ILE ALA ALA LYS ALA VAL ALA PHE GLY GLU ALA SEQRES 22 A 405 LEU GLN ASP ASP PHE LYS ALA TYR ALA LYS ARG VAL VAL SEQRES 23 A 405 ASP ASN ALA LYS ARG LEU ALA SER ALA LEU GLN ASN GLU SEQRES 24 A 405 GLY PHE THR LEU VAL SER GLY GLY THR ASP ASN HIS LEU SEQRES 25 A 405 LEU LEU VAL ASP LEU ARG PRO GLN GLN LEU THR GLY LYS SEQRES 26 A 405 THR ALA GLU LYS VAL LEU ASP GLU VAL GLY ILE THR VAL SEQRES 27 A 405 ASN LYS ASN THR ILE PRO TYR ASP PRO GLU SER PRO GLY SEQRES 28 A 405 VAL THR SER GLY ILE ARG ILE GLY THR ALA ALA VAL THR SEQRES 29 A 405 THR ARG GLY PHE GLY LEU GLU GLU MET ASP GLU ILE ALA SEQRES 30 A 405 ALA ILE ILE GLY LEU VAL LEU LYS ASN VAL GLY SER GLU SEQRES 31 A 405 GLN ALA LEU GLU GLU ALA ARG GLN ARG VAL ALA ALA LEU SEQRES 32 A 405 THR ASP SEQRES 1 B 405 MET LYS TYR LEU PRO GLN GLN ASP PRO GLN VAL PHE ALA SEQRES 2 B 405 ALA ILE GLU GLN GLU ARG LYS ARG GLN HIS ALA LYS ILE SEQRES 3 B 405 GLU LEU ILE ALA SER GLU ASN PHE VAL SER ARG ALA VAL SEQRES 4 B 405 MET GLU ALA GLN GLY SER VAL LEU THR ASN LYS TYR ALA SEQRES 5 B 405 GLU GLY TYR PRO GLY ARG ARG TYR TYR GLY GLY CYS GLU SEQRES 6 B 405 TYR VAL ASP ILE VAL GLU GLU LEU ALA ARG GLU ARG ALA SEQRES 7 B 405 LYS GLN LEU PHE GLY ALA GLU HIS ALA ASN VAL GLN PRO SEQRES 8 B 405 HIS SER GLY ALA GLN ALA ASN MET ALA VAL TYR PHE THR SEQRES 9 B 405 VAL LEU GLU HIS GLY ASP THR VAL LEU GLY MET ASN LEU SEQRES 10 B 405 SER HIS GLY GLY HIS LEU THR HIS GLY SER PRO VAL ASN SEQRES 11 B 405 PHE SER GLY VAL GLN TYR ASN PHE VAL ALA TYR GLY VAL SEQRES 12 B 405 ASP PRO GLU THR HIS VAL ILE ASP TYR ASP ASP VAL ARG SEQRES 13 B 405 GLU LYS ALA ARG LEU HIS ARG PRO LYS LEU ILE VAL ALA SEQRES 14 B 405 ALA ALA SER ALA TYR PRO ARG ILE ILE ASP PHE ALA LYS SEQRES 15 B 405 PHE ARG GLU ILE ALA ASP GLU VAL GLY ALA TYR LEU MET SEQRES 16 B 405 VAL ASP MET ALA HIS ILE ALA GLY LEU VAL ALA ALA GLY SEQRES 17 B 405 LEU HIS PRO ASN PRO VAL PRO TYR ALA HIS PHE VAL THR SEQRES 18 B 405 THR THR THR HIS LYS THR LEU ARG GLY PRO ARG GLY GLY SEQRES 19 B 405 MET ILE LEU CYS GLN GLU GLN PHE ALA LYS GLN ILE ASP SEQRES 20 B 405 LYS ALA ILE PHE PRO GLY ILE GLN GLY GLY PRO LEU MET SEQRES 21 B 405 HIS VAL ILE ALA ALA LYS ALA VAL ALA PHE GLY GLU ALA SEQRES 22 B 405 LEU GLN ASP ASP PHE LYS ALA TYR ALA LYS ARG VAL VAL SEQRES 23 B 405 ASP ASN ALA LYS ARG LEU ALA SER ALA LEU GLN ASN GLU SEQRES 24 B 405 GLY PHE THR LEU VAL SER GLY GLY THR ASP ASN HIS LEU SEQRES 25 B 405 LEU LEU VAL ASP LEU ARG PRO GLN GLN LEU THR GLY LYS SEQRES 26 B 405 THR ALA GLU LYS VAL LEU ASP GLU VAL GLY ILE THR VAL SEQRES 27 B 405 ASN LYS ASN THR ILE PRO TYR ASP PRO GLU SER PRO GLY SEQRES 28 B 405 VAL THR SER GLY ILE ARG ILE GLY THR ALA ALA VAL THR SEQRES 29 B 405 THR ARG GLY PHE GLY LEU GLU GLU MET ASP GLU ILE ALA SEQRES 30 B 405 ALA ILE ILE GLY LEU VAL LEU LYS ASN VAL GLY SER GLU SEQRES 31 B 405 GLN ALA LEU GLU GLU ALA ARG GLN ARG VAL ALA ALA LEU SEQRES 32 B 405 THR ASP HET GLY A 502 5 HET PLP A 501 15 HET FFO A 505 34 HET GLY B 502 5 HET PLP B 501 15 HET FFO B 505 34 HET MRD B 701 8 HETNAM GLY GLYCINE HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM FFO N-[4-({[(6S)-2-AMINO-5-FORMYL-4-OXO-3,4,5,6,7,8- HETNAM 2 FFO HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L- HETNAM 3 FFO GLUTAMIC ACID HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL HETSYN PLP VITAMIN B6 PHOSPHATE HETSYN FFO [6S]-5-FORMYL-TETRAHYDROFOLATE; 6S-FOLINIC ACID FORMUL 3 GLY 2(C2 H5 N O2) FORMUL 4 PLP 2(C8 H10 N O6 P) FORMUL 5 FFO 2(C20 H23 N7 O7) FORMUL 9 MRD C6 H14 O2 FORMUL 10 HOH *24(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 TYR A 66 GLY A 83 1 18 HELIX 6 6 SER A 93 LEU A 106 1 14 HELIX 7 7 HIS A 122 GLY A 126 5 5 HELIX 8 8 ASN A 130 TYR A 136 1 7 HELIX 9 9 ASP A 151 ARG A 163 1 13 HELIX 10 10 ASP A 179 VAL A 190 1 12 HELIX 11 11 ILE A 201 ALA A 207 1 7 HELIX 12 12 PRO A 213 ALA A 217 5 5 HELIX 13 13 PHE A 242 PHE A 251 1 10 HELIX 14 14 LEU A 259 GLN A 275 1 17 HELIX 15 15 GLN A 275 GLU A 299 1 25 HELIX 16 16 SER A 305 GLY A 307 5 3 HELIX 17 17 THR A 323 GLY A 335 1 13 HELIX 18 18 THR A 360 ARG A 366 1 7 HELIX 19 19 GLY A 369 LYS A 385 1 17 HELIX 20 20 SER A 389 ASP A 405 1 17 HELIX 21 21 TYR B 3 ASP B 8 1 6 HELIX 22 22 ASP B 8 LYS B 25 1 18 HELIX 23 23 SER B 36 GLY B 44 1 9 HELIX 24 24 SER B 45 LYS B 50 5 6 HELIX 25 25 CYS B 64 GLY B 83 1 20 HELIX 26 26 SER B 93 LEU B 106 1 14 HELIX 27 27 HIS B 122 GLY B 126 5 5 HELIX 28 28 ASN B 130 TYR B 136 1 7 HELIX 29 29 ASP B 151 ARG B 163 1 13 HELIX 30 30 ASP B 179 VAL B 190 1 12 HELIX 31 31 ILE B 201 ALA B 207 1 7 HELIX 32 32 PHE B 242 PHE B 251 1 10 HELIX 33 33 LEU B 259 GLN B 275 1 17 HELIX 34 34 GLN B 275 GLU B 299 1 25 HELIX 35 35 SER B 305 GLY B 307 5 3 HELIX 36 36 ARG B 318 GLN B 321 5 4 HELIX 37 37 THR B 323 GLY B 335 1 13 HELIX 38 38 THR B 360 ARG B 366 1 7 HELIX 39 39 GLY B 369 ASN B 386 1 18 HELIX 40 40 SER B 389 ASP B 405 1 17 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 LYS A 340 -1 O ASN A 339 N ARG A 357 SHEET 1 BA 2 ILE B 26 GLU B 27 0 SHEET 2 BA 2 ILE B 336 THR B 337 1 N THR B 337 O ILE B 26 SHEET 1 BB 2 GLY B 54 TYR B 55 0 SHEET 2 BB 2 ARG B 58 ARG B 59 -1 O ARG B 58 N TYR B 55 SHEET 1 BC 7 HIS B 86 ASN B 88 0 SHEET 2 BC 7 GLY B 234 CYS B 238 -1 O ILE B 236 N ASN B 88 SHEET 3 BC 7 PHE B 219 THR B 223 -1 O VAL B 220 N LEU B 237 SHEET 4 BC 7 TYR B 193 ASP B 197 1 O LEU B 194 N PHE B 219 SHEET 5 BC 7 LEU B 166 ALA B 169 1 O ILE B 167 N MET B 195 SHEET 6 BC 7 THR B 111 MET B 115 1 O LEU B 113 N VAL B 168 SHEET 7 BC 7 ASN B 137 TYR B 141 1 O ASN B 137 N VAL B 112 SHEET 1 BD 4 THR B 302 LEU B 303 0 SHEET 2 BD 4 LEU B 312 ASP B 316 -1 O ASP B 316 N THR B 302 SHEET 3 BD 4 GLY B 355 GLY B 359 -1 O ILE B 356 N VAL B 315 SHEET 4 BD 4 ASN B 339 ASN B 341 -1 O ASN B 339 N ARG B 357 LINK C4A PLP A 501 N GLY A 502 1555 1555 1.23 LINK C4A PLP B 501 N GLY B 502 1555 1555 1.23 CISPEP 1 PHE A 251 PRO A 252 0 7.57 CISPEP 2 PHE B 251 PRO B 252 0 3.09 SITE 1 AC1 16 SER A 93 GLY A 94 ALA A 95 HIS A 122 SITE 2 AC1 16 ALA A 171 SER A 172 ASP A 197 ALA A 199 SITE 3 AC1 16 HIS A 200 THR A 223 HIS A 225 LYS A 226 SITE 4 AC1 16 GLY A 502 TYR B 51 GLY B 256 GLY B 257 SITE 1 AC2 8 SER A 31 HIS A 200 LYS A 226 ARG A 357 SITE 2 AC2 8 PLP A 501 TYR B 51 TYR B 61 FFO B 505 SITE 1 AC3 17 GLU A 53 TYR A 60 TYR A 61 LYS A 248 SITE 2 AC3 17 PHE A 251 LEU B 117 GLY B 120 GLY B 121 SITE 3 AC3 17 HIS B 122 LEU B 123 VAL B 129 SER B 172 SITE 4 AC3 17 ASN B 341 SER B 349 PRO B 350 GLY B 351 SITE 5 AC3 17 GLY B 502 SITE 1 AC4 17 TYR A 51 GLY A 256 GLY A 257 SER B 93 SITE 2 AC4 17 GLY B 94 ALA B 95 HIS B 122 ALA B 171 SITE 3 AC4 17 SER B 172 ASP B 197 ALA B 199 HIS B 200 SITE 4 AC4 17 THR B 223 HIS B 225 LYS B 226 GLY B 502 SITE 5 AC4 17 HOH B2003 SITE 1 AC5 8 TYR A 51 TYR A 61 FFO A 505 SER B 31 SITE 2 AC5 8 HIS B 200 LYS B 226 ARG B 357 PLP B 501 SITE 1 AC6 17 LEU A 117 GLY A 120 GLY A 121 HIS A 122 SITE 2 AC6 17 LEU A 123 VAL A 129 ASN A 339 ASN A 341 SITE 3 AC6 17 SER A 349 PRO A 350 GLY A 351 ARG A 357 SITE 4 AC6 17 GLY A 502 GLU B 53 TYR B 60 TYR B 61 SITE 5 AC6 17 PHE B 251 SITE 1 AC7 2 TYR A 136 GLN B 135 CRYST1 57.382 103.483 61.959 90.00 90.33 90.00 P 1 21 1 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 0.017427 0.000000 0.000100 0.00000 SCALE2 0.000000 0.009663 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016140 0.00000