HEADER LYASE 01-NOV-10 2XW6 TITLE THE CRYSTAL STRUCTURE OF METHYLGLYOXAL SYNTHASE FROM THERMUS SP. GH5 TITLE 2 BOUND TO PHOSPHATE ION. COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYLGLYOXAL SYNTHASE; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: MGS; COMPND 5 EC: 4.2.3.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS SP. GH5; SOURCE 3 ORGANISM_TAXID: 405418; 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: PET28A KEYWDS LYASE EXPDTA X-RAY DIFFRACTION AUTHOR A.SHAHSAVAR,M.ERFANI MOGHADDAM,S.V.ANTONYUK,K.KHAJEH,H.NADERI-MANESH REVDAT 4 20-DEC-23 2XW6 1 REMARK REVDAT 3 22-MAY-19 2XW6 1 REMARK REVDAT 2 08-MAY-19 2XW6 1 REMARK REVDAT 1 09-NOV-11 2XW6 0 JRNL AUTH A.SHAHSAVAR,M.ERFANI MOGHADDAM,S.V.ANTONYUK,K.KHAJEH, JRNL AUTH 2 H.NADERI-MANESH JRNL TITL ATOMIC RESOLUTION STRUCTURE OF METHYLGLYOXAL SYNTHASE FROM JRNL TITL 2 THERMUS SP. GH5 BOUND TO PHOSPHATE: INSIGHTS INTO THE JRNL TITL 3 DISTINCTIVE EFFECTS OF PHOSPHATE ON THE ENZYME STRUCTURE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.08 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.129 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.129 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.161 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 7806 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 148053 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.129 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.117 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.149 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 6590 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 148053 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2903 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 463 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 3293.8 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 2925.6 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 58 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 33060 REMARK 3 NUMBER OF RESTRAINTS : 43564 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 ANGLE DISTANCES (A) : 0.034 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.030 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.092 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.093 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.083 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.051 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.109 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2XW6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1290046007. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 156269 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.080 REMARK 200 RESOLUTION RANGE LOW (A) : 42.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.54000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 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: PDB ENTRY 1WO8 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE OBTAINED USING REMARK 280 MICROBATCH METHOD AT 4C. CRYSTALLIZATION DROPS WERE MADE BY REMARK 280 MIXING 2 MICROLITER OF A 7.8 MG/ML PROTEIN SOLUTION IN 50 MM REMARK 280 TRIS-HCL, 300 MM NACL, 160 MM IMIDAZOLE AND 20% GLYCEROL WITH REMARK 280 EQUAL AMOUNT OF CRYSTALLIZATION SOLUTION CONTAINING 0.1 M TRIS- REMARK 280 HCL (PH 8.0), 29% W/V POLYETHYLENE GLYCOL (PEG) 4000., REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 60.21550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.21550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 27.31800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 57.58600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 27.31800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 57.58600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 60.21550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 27.31800 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 57.58600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 60.21550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 27.31800 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 57.58600 REMARK 290 SMTRY3 8 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 13170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -113.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 -54.63600 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -60.21550 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 129 REMARK 465 GLN A 130 REMARK 465 GLY A 131 REMARK 465 GLN A 132 REMARK 465 TYR B 126 REMARK 465 GLN B 127 REMARK 465 THR B 128 REMARK 465 PRO B 129 REMARK 465 GLN B 130 REMARK 465 GLY B 131 REMARK 465 GLN B 132 REMARK 465 SER C -1 REMARK 465 HIS C 0 REMARK 465 GLY C 125 REMARK 465 TYR C 126 REMARK 465 GLN C 127 REMARK 465 THR C 128 REMARK 465 PRO C 129 REMARK 465 GLN C 130 REMARK 465 GLY C 131 REMARK 465 GLN C 132 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 HIS A 0 CE1 HIS A 0 NE2 -0.072 REMARK 500 SER B 55 CB SER B 55 OG -0.082 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 HIS A 0 C - N - CA ANGL. DEV. = 31.4 DEGREES REMARK 500 HIS A 0 CA - CB - CG ANGL. DEV. = 15.3 DEGREES REMARK 500 HIS A 9 CG - ND1 - CE1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG A 22 CD - NE - CZ ANGL. DEV. = 12.9 DEGREES REMARK 500 ARG A 40 CD - NE - CZ ANGL. DEV. = 10.8 DEGREES REMARK 500 ARG A 40 NE - CZ - NH1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG A 41 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 GLY A 47 O - C - N ANGL. DEV. = -9.7 DEGREES REMARK 500 LEU A 48 C - N - CA ANGL. DEV. = 17.1 DEGREES REMARK 500 ARG A 67 CD - NE - CZ ANGL. DEV. = 16.3 DEGREES REMARK 500 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 67 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 67 NE - CZ - NH2 ANGL. DEV. = -6.6 DEGREES REMARK 500 PHE A 78 CB - CG - CD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 97 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 GLY A 125 C - N - CA ANGL. DEV. = -16.5 DEGREES REMARK 500 HIS B 0 C - N - CA ANGL. DEV. = 15.8 DEGREES REMARK 500 ARG B 2 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG B 2 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG B 22 CA - CB - CG ANGL. DEV. = 13.8 DEGREES REMARK 500 ARG B 22 CD - NE - CZ ANGL. DEV. = 21.2 DEGREES REMARK 500 ARG B 22 NE - CZ - NH1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG B 24 CD - NE - CZ ANGL. DEV. = 15.1 DEGREES REMARK 500 ARG B 24 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG B 24 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG B 24 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG B 29 CD - NE - CZ ANGL. DEV. = 9.2 DEGREES REMARK 500 ARG B 29 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG B 29 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG B 40 CD - NE - CZ ANGL. DEV. = 11.7 DEGREES REMARK 500 ARG B 41 CD - NE - CZ ANGL. DEV. = 14.9 DEGREES REMARK 500 LEU B 48 C - N - CA ANGL. DEV. = 16.6 DEGREES REMARK 500 ASP B 61 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG B 67 NE - CZ - NH1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG B 67 NE - CZ - NH2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG B 67 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG B 72 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 PHE B 78 CB - CG - CD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG B 80 NE - CZ - NH1 ANGL. DEV. = 8.7 DEGREES REMARK 500 ARG B 80 NE - CZ - NH2 ANGL. DEV. = -7.1 DEGREES REMARK 500 ARG B 97 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG C 2 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG C 29 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG C 40 CD - NE - CZ ANGL. DEV. = 12.3 DEGREES REMARK 500 ARG C 41 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 GLY C 47 O - C - N ANGL. DEV. = -10.4 DEGREES REMARK 500 ARG C 67 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG C 67 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG C 72 CD - NE - CZ ANGL. DEV. = 18.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 54 ANGLE DEVIATIONS. 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 SER A -1 HIS A 0 -149.21 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 C2027 DISTANCE = 6.10 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1131 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 1131 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 C 1131 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2X8W RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF METHYLGLYOXAL SYNTHASE FROM THERMUS SP. REMARK 900 GH5 BOUND TO MALONATE. DBREF 2XW6 A 1 132 UNP B3VH91 B3VH91_9DEIN 1 132 DBREF 2XW6 B 1 132 UNP B3VH91 B3VH91_9DEIN 1 132 DBREF 2XW6 C 1 132 UNP B3VH91 B3VH91_9DEIN 1 132 SEQADV 2XW6 SER A -1 UNP B3VH91 EXPRESSION TAG SEQADV 2XW6 HIS A 0 UNP B3VH91 EXPRESSION TAG SEQADV 2XW6 SER B -1 UNP B3VH91 EXPRESSION TAG SEQADV 2XW6 HIS B 0 UNP B3VH91 EXPRESSION TAG SEQADV 2XW6 SER C -1 UNP B3VH91 EXPRESSION TAG SEQADV 2XW6 HIS C 0 UNP B3VH91 EXPRESSION TAG SEQRES 1 A 134 SER HIS MET ARG ALA LEU ALA LEU ILE ALA HIS ASP ALA SEQRES 2 A 134 LYS LYS GLU GLU MET VAL ALA PHE CYS GLN ARG HIS ARG SEQRES 3 A 134 GLU VAL LEU ALA ARG PHE PRO LEU VAL ALA THR GLY THR SEQRES 4 A 134 THR GLY ARG ARG ILE GLU GLU ALA THR GLY LEU THR VAL SEQRES 5 A 134 GLU LYS LEU LEU SER GLY PRO LEU GLY GLY ASP GLN GLN SEQRES 6 A 134 MET GLY ALA ARG VAL ALA GLU GLY ARG ILE LEU ALA VAL SEQRES 7 A 134 ILE PHE PHE ARG ASP PRO LEU THR ALA GLN PRO HIS GLU SEQRES 8 A 134 PRO ASP VAL GLN ALA LEU LEU ARG VAL CYS ASP VAL HIS SEQRES 9 A 134 GLY VAL PRO LEU ALA THR ASN PRO MET ALA ALA GLU ALA SEQRES 10 A 134 LEU ILE PRO TRP LEU GLN SER LEU VAL GLY TYR GLN THR SEQRES 11 A 134 PRO GLN GLY GLN SEQRES 1 B 134 SER HIS MET ARG ALA LEU ALA LEU ILE ALA HIS ASP ALA SEQRES 2 B 134 LYS LYS GLU GLU MET VAL ALA PHE CYS GLN ARG HIS ARG SEQRES 3 B 134 GLU VAL LEU ALA ARG PHE PRO LEU VAL ALA THR GLY THR SEQRES 4 B 134 THR GLY ARG ARG ILE GLU GLU ALA THR GLY LEU THR VAL SEQRES 5 B 134 GLU LYS LEU LEU SER GLY PRO LEU GLY GLY ASP GLN GLN SEQRES 6 B 134 MET GLY ALA ARG VAL ALA GLU GLY ARG ILE LEU ALA VAL SEQRES 7 B 134 ILE PHE PHE ARG ASP PRO LEU THR ALA GLN PRO HIS GLU SEQRES 8 B 134 PRO ASP VAL GLN ALA LEU LEU ARG VAL CYS ASP VAL HIS SEQRES 9 B 134 GLY VAL PRO LEU ALA THR ASN PRO MET ALA ALA GLU ALA SEQRES 10 B 134 LEU ILE PRO TRP LEU GLN SER LEU VAL GLY TYR GLN THR SEQRES 11 B 134 PRO GLN GLY GLN SEQRES 1 C 134 SER HIS MET ARG ALA LEU ALA LEU ILE ALA HIS ASP ALA SEQRES 2 C 134 LYS LYS GLU GLU MET VAL ALA PHE CYS GLN ARG HIS ARG SEQRES 3 C 134 GLU VAL LEU ALA ARG PHE PRO LEU VAL ALA THR GLY THR SEQRES 4 C 134 THR GLY ARG ARG ILE GLU GLU ALA THR GLY LEU THR VAL SEQRES 5 C 134 GLU LYS LEU LEU SER GLY PRO LEU GLY GLY ASP GLN GLN SEQRES 6 C 134 MET GLY ALA ARG VAL ALA GLU GLY ARG ILE LEU ALA VAL SEQRES 7 C 134 ILE PHE PHE ARG ASP PRO LEU THR ALA GLN PRO HIS GLU SEQRES 8 C 134 PRO ASP VAL GLN ALA LEU LEU ARG VAL CYS ASP VAL HIS SEQRES 9 C 134 GLY VAL PRO LEU ALA THR ASN PRO MET ALA ALA GLU ALA SEQRES 10 C 134 LEU ILE PRO TRP LEU GLN SER LEU VAL GLY TYR GLN THR SEQRES 11 C 134 PRO GLN GLY GLN HET PO4 A1131 5 HET PO4 B1131 5 HET PO4 C1131 5 HETNAM PO4 PHOSPHATE ION FORMUL 4 PO4 3(O4 P 3-) FORMUL 7 HOH *463(H2 O) HELIX 1 1 LYS A 12 HIS A 23 1 12 HELIX 2 2 HIS A 23 ALA A 28 1 6 HELIX 3 3 THR A 35 GLY A 47 1 13 HELIX 4 4 SER A 55 LEU A 58 5 4 HELIX 5 5 GLY A 59 GLU A 70 1 12 HELIX 6 6 VAL A 92 GLY A 103 1 12 HELIX 7 7 ASN A 109 SER A 122 1 14 HELIX 8 8 LYS B 12 HIS B 23 1 12 HELIX 9 9 HIS B 23 ALA B 28 1 6 HELIX 10 10 THR B 35 GLY B 47 1 13 HELIX 11 11 SER B 55 LEU B 58 5 4 HELIX 12 12 GLY B 59 GLU B 70 1 12 HELIX 13 13 VAL B 92 GLY B 103 1 12 HELIX 14 14 ASN B 109 VAL B 124 1 16 HELIX 15 15 LYS C 12 HIS C 23 1 12 HELIX 16 16 HIS C 23 ALA C 28 1 6 HELIX 17 17 THR C 35 GLY C 47 1 13 HELIX 18 18 SER C 55 LEU C 58 5 4 HELIX 19 19 GLY C 59 GLU C 70 1 12 HELIX 20 20 VAL C 92 GLY C 103 1 12 HELIX 21 21 ASN C 109 VAL C 124 1 16 SHEET 1 AA 5 GLU A 51 LYS A 52 0 SHEET 2 AA 5 LEU A 32 ALA A 34 1 O LEU A 32 N GLU A 51 SHEET 3 AA 5 ALA A 3 ALA A 8 1 O LEU A 4 N VAL A 33 SHEET 4 AA 5 ILE A 73 PHE A 79 1 N LEU A 74 O ALA A 3 SHEET 5 AA 5 LEU A 106 ALA A 107 1 O ALA A 107 N PHE A 78 SHEET 1 BA 5 GLU B 51 LYS B 52 0 SHEET 2 BA 5 LEU B 32 ALA B 34 1 O LEU B 32 N GLU B 51 SHEET 3 BA 5 ALA B 3 ALA B 8 1 O LEU B 4 N VAL B 33 SHEET 4 BA 5 ILE B 73 PHE B 79 1 N LEU B 74 O ALA B 3 SHEET 5 BA 5 LEU B 106 ALA B 107 1 O ALA B 107 N PHE B 78 SHEET 1 CA 5 GLU C 51 LYS C 52 0 SHEET 2 CA 5 LEU C 32 ALA C 34 1 O LEU C 32 N GLU C 51 SHEET 3 CA 5 ALA C 3 ALA C 8 1 O LEU C 4 N VAL C 33 SHEET 4 CA 5 ILE C 73 PHE C 79 1 N LEU C 74 O ALA C 3 SHEET 5 CA 5 LEU C 106 ALA C 107 1 O ALA C 107 N PHE C 78 SITE 1 AC1 8 LYS A 13 THR A 35 THR A 37 THR A 38 SITE 2 AC1 8 SER A 55 GLY A 56 HOH A2168 HOH A2169 SITE 1 AC2 10 LYS B 13 THR B 35 THR B 37 THR B 38 SITE 2 AC2 10 SER B 55 GLY B 56 PRO B 57 HOH B2070 SITE 3 AC2 10 HOH B2150 HOH B2151 SITE 1 AC3 8 LYS C 13 THR C 35 THR C 37 THR C 38 SITE 2 AC3 8 SER C 55 GLY C 56 HOH C2142 HOH C2143 CRYST1 54.636 115.172 120.431 90.00 90.00 90.00 C 2 2 21 24 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 0.018303 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008683 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008304 0.00000