HEADER TRANSFERASE 16-JAN-05 1YJY TITLE K226M MUTANT OF SERINE HYDROXYMETHYLTRANSFERASE FROM B. TITLE 2 STEAROTHERMOPHILUS, COMPLEX WITH SERINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE HYDROXYMETHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SERINE METHYLASE; COMPND 5 EC: 2.1.2.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1422; SOURCE 4 GENE: SHMT; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PRSETC KEYWDS SHMT, MUTANT, CATALYSIS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.BHAVANI,V.TRIVEDI,V.R.JALA,H.S.SUBRAMANYA,P.KAUL,K.PURNIMA, AUTHOR 2 V.PRAKASH,R.N.APPAJI,H.S.SAVITHRI REVDAT 3 13-JUL-11 1YJY 1 VERSN REVDAT 2 24-FEB-09 1YJY 1 VERSN REVDAT 1 31-MAY-05 1YJY 0 JRNL AUTH S.BHAVANI,V.TRIVEDI,V.R.JALA,H.S.SUBRAMANYA,P.KAUL, JRNL AUTH 2 K.PURNIMA,V.PRAKASH,R.N.APPAJI,H.S.SAVITHRI JRNL TITL ROLE OF LYS-226 IN THE CATALYTIC MECHANISM OF BACILLUS JRNL TITL 2 STEAROTHERMOPHILUS SERINE HYDROXYMETHYLTRANSFERASE-CRYSTAL JRNL TITL 3 STRUCTURE AND KINETIC STUDIES JRNL REF BIOCHEMISTRY V. 44 6929 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 15865438 JRNL DOI 10.1021/BI047800X REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 16950 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 853 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3115 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 137 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.013 ; NULL REMARK 3 ANGLE DISTANCE (A) : 0.036 ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.063 ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1YJY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-JAN-05. REMARK 100 THE RCSB ID CODE IS RCSB031599. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAR-02 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS 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 : 18477 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.14500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1KKJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES, MPD, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K 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 30.49050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.13800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.49050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.13800 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 300 REMARK: THE SECOND PART OF THE BIOLOGICAL ASSEMBLY IS GENERATED BY REMARK 300 THE TWO FOLD AXIS : -X, -Y, Z. 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 8450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 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 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 PRO A 406 REMARK 465 THR A 407 REMARK 465 SER A 408 REMARK 465 ARG A 409 REMARK 465 SER A 410 REMARK 465 ALA A 411 REMARK 465 ALA A 412 REMARK 465 GLY A 413 REMARK 465 THR A 414 REMARK 465 MET A 415 REMARK 465 GLU A 416 REMARK 465 PHE A 417 REMARK 465 GLU A 418 REMARK 465 ALA A 419 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 O THR A 48 O HOH A 618 1.62 REMARK 500 N ASN A 49 O HOH A 618 1.85 REMARK 500 C THR A 48 O HOH A 618 1.94 REMARK 500 CA ASN A 49 O HOH A 618 1.95 REMARK 500 NE2 GLN A 17 O HOH A 681 2.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 THR A 48 C THR A 48 O 0.154 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 GLN A 17 CB - CA - C ANGL. DEV. = -14.1 DEGREES REMARK 500 ARG A 37 CD - NE - CZ ANGL. DEV. = 12.5 DEGREES REMARK 500 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG A 37 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 THR A 48 N - CA - CB ANGL. DEV. = 22.0 DEGREES REMARK 500 THR A 48 N - CA - C ANGL. DEV. = -22.5 DEGREES REMARK 500 THR A 48 CA - C - O ANGL. DEV. = -19.4 DEGREES REMARK 500 ASN A 49 N - CA - CB ANGL. DEV. = 11.0 DEGREES REMARK 500 ASN A 49 N - CA - C ANGL. DEV. = 17.2 DEGREES REMARK 500 THR A 48 CA - C - N ANGL. DEV. = 21.3 DEGREES REMARK 500 ASN A 49 C - N - CA ANGL. DEV. = 17.3 DEGREES REMARK 500 ARG A 59 CD - NE - CZ ANGL. DEV. = 10.8 DEGREES REMARK 500 ARG A 77 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 77 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 TYR A 102 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 TYR A 102 CB - CG - CD1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG A 163 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 229 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 PHE A 251 CA - C - O ANGL. DEV. = -17.2 DEGREES REMARK 500 PRO A 252 CA - N - CD ANGL. DEV. = -8.9 DEGREES REMARK 500 PRO A 252 N - CA - CB ANGL. DEV. = 7.5 DEGREES REMARK 500 ASP A 276 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASN A 339 CB - CA - C ANGL. DEV. = -12.7 DEGREES REMARK 500 ARG A 397 CD - NE - CZ ANGL. DEV. = 9.0 DEGREES REMARK 500 ARG A 397 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 397 NE - CZ - NH2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG A 399 NE - CZ - NH2 ANGL. DEV. = -4.1 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 ASN A 49 -5.28 -56.89 REMARK 500 ALA A 52 45.38 -144.24 REMARK 500 ARG A 58 52.15 -146.73 REMARK 500 ALA A 170 174.27 107.41 REMARK 500 ALA A 173 52.50 -145.63 REMARK 500 MET A 226 -104.22 -95.16 REMARK 500 ASN A 310 -138.74 -138.19 REMARK 500 THR A 353 162.45 70.39 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 PHE A 251 PRO A 252 52.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 THR A 48 15.27 REMARK 500 ASN A 49 -13.86 REMARK 500 PHE A 251 20.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ASN A 49 13.6 L L OUTSIDE RANGE REMARK 500 ALA A 170 25.0 L L OUTSIDE RANGE 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SER A 601 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YJS RELATED DB: PDB REMARK 900 K226Q MUTANT OF SERINE HYDROXYMETHYLTRANSFERASE COMPLEXED REMARK 900 WITH GLYCINE REMARK 900 RELATED ID: 1YJZ RELATED DB: PDB REMARK 900 K226M MUTANT OF SERINE HYDROXYMETHYLTRANSFERASE DBREF 1YJY A 1 419 UNP Q7SIB6 Q7SIB6_BACST 1 419 SEQRES 1 A 419 MET LYS TYR LEU PRO GLN GLN ASP PRO GLN VAL PHE ALA SEQRES 2 A 419 ALA ILE GLU GLN GLU ARG LYS ARG GLN HIS ALA LYS ILE SEQRES 3 A 419 GLU LEU ILE ALA SER GLU ASN PHE VAL SER ARG ALA VAL SEQRES 4 A 419 MET GLU ALA GLN GLY SER VAL LEU THR ASN LYS TYR ALA SEQRES 5 A 419 GLU GLY TYR PRO GLY ARG ARG TYR TYR GLY GLY CYS GLU SEQRES 6 A 419 TYR VAL ASP ILE VAL GLU GLU LEU ALA ARG GLU ARG ALA SEQRES 7 A 419 LYS GLN LEU PHE GLY ALA GLU HIS ALA ASN VAL GLN PRO SEQRES 8 A 419 HIS SER GLY ALA GLN ALA ASN MET ALA VAL TYR PHE THR SEQRES 9 A 419 VAL LEU GLU HIS GLY ASP THR VAL LEU GLY MET ASN LEU SEQRES 10 A 419 SER HIS GLY GLY HIS LEU THR HIS GLY SER PRO VAL ASN SEQRES 11 A 419 PHE SER GLY VAL GLN TYR ASN PHE VAL ALA TYR GLY VAL SEQRES 12 A 419 ASP PRO GLU THR HIS VAL ILE ASP TYR ASP ASP VAL ARG SEQRES 13 A 419 GLU LYS ALA ARG LEU HIS ARG PRO LYS LEU ILE VAL ALA SEQRES 14 A 419 ALA ALA SER ALA TYR PRO ARG ILE ILE ASP PHE ALA LYS SEQRES 15 A 419 PHE ARG GLU ILE ALA ASP GLU VAL GLY ALA TYR LEU MET SEQRES 16 A 419 VAL ASP MET ALA HIS ILE ALA GLY LEU VAL ALA ALA GLY SEQRES 17 A 419 LEU HIS PRO ASN PRO VAL PRO TYR ALA HIS PHE VAL THR SEQRES 18 A 419 THR THR THR HIS MET THR LEU ARG GLY PRO ARG GLY GLY SEQRES 19 A 419 MET ILE LEU CYS GLN GLU GLN PHE ALA LYS GLN ILE ASP SEQRES 20 A 419 LYS ALA ILE PHE PRO GLY ILE GLN GLY GLY PRO LEU MET SEQRES 21 A 419 HIS VAL ILE ALA ALA LYS ALA VAL ALA PHE GLY GLU ALA SEQRES 22 A 419 LEU GLN ASP ASP PHE LYS ALA TYR ALA LYS ARG VAL VAL SEQRES 23 A 419 ASP ASN ALA LYS ARG LEU ALA SER ALA LEU GLN ASN GLU SEQRES 24 A 419 GLY PHE THR LEU VAL SER GLY GLY THR ASP ASN HIS LEU SEQRES 25 A 419 LEU LEU VAL ASP LEU ARG PRO GLN GLN LEU THR GLY LYS SEQRES 26 A 419 THR ALA GLU LYS VAL LEU ASP GLU VAL GLY ILE THR VAL SEQRES 27 A 419 ASN LYS ASN THR ILE PRO TYR ASP PRO GLU SER PRO PHE SEQRES 28 A 419 VAL THR SER GLY ILE ARG ILE GLY THR ALA ALA VAL THR SEQRES 29 A 419 THR ARG GLY PHE GLY LEU GLU GLU MET ASP GLU ILE ALA SEQRES 30 A 419 ALA ILE ILE GLY LEU VAL LEU LYS ASN VAL GLY SER GLU SEQRES 31 A 419 GLN ALA LEU GLU GLU ALA ARG GLN ARG VAL ALA ALA LEU SEQRES 32 A 419 THR ASP PRO THR SER ARG SER ALA ALA GLY THR MET GLU SEQRES 33 A 419 PHE GLU ALA HET PLP A 501 15 HET SER A 601 7 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM SER SERINE HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 2 PLP C8 H10 N O6 P FORMUL 2 SER C3 H7 N O3 FORMUL 3 HOH *137(H2 O) HELIX 1 1 LYS A 2 ASP A 8 1 7 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 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 ARG A 318 GLN A 321 5 4 HELIX 18 18 THR A 323 VAL A 334 1 12 HELIX 19 19 THR A 360 ARG A 366 1 7 HELIX 20 20 GLY A 369 LYS A 385 1 17 HELIX 21 21 SER A 389 ASP A 405 1 17 SHEET 1 A 2 ILE A 26 GLU A 27 0 SHEET 2 A 2 ILE A 336 THR A 337 1 O THR A 337 N ILE A 26 SHEET 1 B 2 GLY A 54 TYR A 55 0 SHEET 2 B 2 ARG A 58 ARG A 59 -1 O ARG A 58 N TYR A 55 SHEET 1 C 7 HIS A 86 ASN A 88 0 SHEET 2 C 7 GLY A 234 CYS A 238 -1 O CYS A 238 N HIS A 86 SHEET 3 C 7 PHE A 219 THR A 223 -1 N VAL A 220 O LEU A 237 SHEET 4 C 7 TYR A 193 ASP A 197 1 N VAL A 196 O PHE A 219 SHEET 5 C 7 LEU A 166 ALA A 169 1 N ILE A 167 O MET A 195 SHEET 6 C 7 THR A 111 MET A 115 1 N LEU A 113 O VAL A 168 SHEET 7 C 7 ASN A 137 TYR A 141 1 O ASN A 137 N VAL A 112 SHEET 1 D 4 THR A 302 LEU A 303 0 SHEET 2 D 4 LEU A 312 ASP A 316 -1 O ASP A 316 N THR A 302 SHEET 3 D 4 GLY A 355 GLY A 359 -1 O ILE A 358 N LEU A 313 SHEET 4 D 4 ASN A 339 LYS A 340 -1 N ASN A 339 O ARG A 357 LINK C4A PLP A 501 N SER A 601 1555 1555 1.34 SITE 1 AC1 18 TYR A 51 SER A 93 GLY A 94 ALA A 95 SITE 2 AC1 18 HIS A 122 SER A 172 ASP A 197 ALA A 199 SITE 3 AC1 18 HIS A 200 THR A 223 HIS A 225 MET A 226 SITE 4 AC1 18 GLY A 256 GLY A 257 SER A 601 HOH A 623 SITE 5 AC1 18 HOH A 637 HOH A 638 SITE 1 AC2 10 SER A 31 GLU A 53 TYR A 61 HIS A 122 SITE 2 AC2 10 SER A 172 HIS A 200 MET A 226 ARG A 357 SITE 3 AC2 10 PLP A 501 HOH A 623 CRYST1 60.981 106.276 56.893 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 0.016399 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009409 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017577 0.00000 MASTER 384 0 2 21 15 0 8 6 0 0 0 33 END