HEADER LYASE 27-JAN-14 4OMA TITLE THE CRYSTAL STRUCTURE OF METHIONINE GAMMA-LYASE FROM CITROBACTER TITLE 2 FREUNDII IN COMPLEX WITH L-CYCLOSERINE PYRIDOXAL-5'-PHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHIONINE GAMMA-LYASE; COMPND 3 CHAIN: A; COMPND 4 EC: 4.4.1.11; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CITROBACTER FREUNDII; SOURCE 3 ORGANISM_TAXID: 546; SOURCE 4 GENE: H922_06139, MEGL; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS AMINOTRANSFERASE CLASS I AND II, METHIONINE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR S.V.REVTOVICH,A.D.NIKULIN,E.A.MOROZOVA,T.V.DEMIDKINA REVDAT 4 20-SEP-23 4OMA 1 REMARK REVDAT 3 21-JAN-15 4OMA 1 JRNL REVDAT 2 03-DEC-14 4OMA 1 JRNL REVDAT 1 26-NOV-14 4OMA 0 JRNL AUTH N.A.KUZNETSOV,N.G.FALEEV,A.A.KUZNETSOVA,E.A.MOROZOVA, JRNL AUTH 2 S.V.REVTOVICH,N.V.ANUFRIEVA,A.D.NIKULIN,O.S.FEDOROVA, JRNL AUTH 3 T.V.DEMIDKINA JRNL TITL PRE-STEADY-STATE KINETIC AND STRUCTURAL ANALYSIS OF JRNL TITL 2 INTERACTION OF METHIONINE GAMMA-LYASE FROM CITROBACTER JRNL TITL 3 FREUNDII WITH INHIBITORS. JRNL REF J.BIOL.CHEM. V. 290 671 2015 JRNL REFN ISSN 0021-9258 JRNL PMID 25398880 JRNL DOI 10.1074/JBC.M114.586511 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 53896 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) : 0.142 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2893 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3808 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.28 REMARK 3 BIN R VALUE (WORKING SET) : 0.2750 REMARK 3 BIN FREE R VALUE SET COUNT : 200 REMARK 3 BIN FREE R VALUE : 0.2930 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2993 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 57 REMARK 3 SOLVENT ATOMS : 266 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.51000 REMARK 3 B22 (A**2) : -2.81000 REMARK 3 B33 (A**2) : -2.70000 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): 0.086 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.081 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.102 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.606 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.983 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3177 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3066 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4314 ; 1.943 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7060 ; 1.014 ; 3.004 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 414 ; 6.350 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 130 ;37.696 ;24.308 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 532 ;12.979 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;18.427 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 495 ; 0.144 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3592 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 683 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1609 ; 4.757 ; 2.596 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1605 ; 4.738 ; 2.592 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2014 ; 5.993 ; 3.912 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2013 ; 5.960 ; 3.910 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1566 ; 6.376 ; 3.023 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1567 ; 6.374 ; 3.025 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2290 ; 7.364 ; 4.370 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3784 ; 7.555 ;22.707 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3676 ; 7.248 ;22.204 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 6240 ; 7.260 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 64 ;48.856 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 6381 ;22.149 ; 5.000 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: NULL REMARK 4 REMARK 4 4OMA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000084671. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.843 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROCESS REMARK 200 DATA SCALING SOFTWARE : PROCESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55080 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.39600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: PDB ENTRY 2RFV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5% PEG2000 MME, 50 MM TRIS-HCL, 0.2 MM REMARK 280 PLP, 0.25% DTT, PH 8.5, SOAKED IN 50 MM L-CYCLOSERINE FOR 7 REMARK 280 MINUTES, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 303K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 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+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 28.13500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 61.44500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 63.30500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 28.13500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 61.44500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 63.30500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 28.13500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 61.44500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 63.30500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 28.13500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 61.44500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 63.30500 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 27720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 46780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -137.0 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 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 694 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 756 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 757 LIES ON A SPECIAL POSITION. 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 A 1 REMARK 465 PHE A 398 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 HOH A 705 O HOH A 760 2.05 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 SER A 339 CB SER A 339 OG 0.093 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 CYS A 4 CA - CB - SG ANGL. DEV. = 8.1 DEGREES REMARK 500 ARG A 256 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 264 NE - CZ - NH1 ANGL. DEV. = 3.0 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 A 57 -51.10 -127.43 REMARK 500 PRO A 161 -79.19 -77.18 REMARK 500 SER A 190 162.98 69.61 REMARK 500 LYS A 210 -127.19 -85.67 REMARK 500 LYS A 210 -127.66 -85.22 REMARK 500 VAL A 236 -60.19 -123.92 REMARK 500 ILE A 241 -61.51 -95.39 REMARK 500 SER A 339 171.52 81.76 REMARK 500 MET A 353 -86.08 -117.60 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 HIS A 206 SER A 207 148.39 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 LCS A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 406 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2RFV RELATED DB: PDB REMARK 900 HIGH RESOLUTION STRUCTURE OF THE L-METHIONINE GAMMA-LYASE HOLOENZYME REMARK 900 RELATED ID: 4HF8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF L-METHIONINE GAMMA-LYASE IN COMPLEX WITH REMARK 900 GLYCINE PYRIDOXAL-5'-PHOSPHATE REMARK 900 RELATED ID: 2DAA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE D-AMINO ACID AMINOTRANSFERASE IN COMPLEX REMARK 900 WITH D-CYCLOSERINE PYRIDOXAL-5'-PHOSPHATE REMARK 900 RELATED ID: 1D7U RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE 2,2-DIALKYLGLYCINE DECARBOXYLASE IN REMARK 900 COMPLEX WITH L-CYCLOSERINE PYRIDOXAL-5'-PHOSPHATE DBREF 4OMA A 1 398 UNP R1FPL7 R1FPL7_CITFR 1 398 SEQRES 1 A 398 MET SER ASP CYS ARG THR TYR GLY PHE ASN THR GLN ILE SEQRES 2 A 398 VAL HIS ALA GLY GLN GLN PRO ASP PRO SER THR GLY ALA SEQRES 3 A 398 LEU SER THR PRO ILE PHE GLN THR SER THR PHE VAL PHE SEQRES 4 A 398 ASP SER ALA GLU GLN GLY ALA ALA ARG PHE ALA LEU GLU SEQRES 5 A 398 GLU SER GLY TYR ILE TYR THR ARG LEU GLY ASN PRO THR SEQRES 6 A 398 THR ASP ALA LEU GLU LYS LYS LEU ALA VAL LEU GLU ARG SEQRES 7 A 398 GLY GLU ALA GLY LEU ALA THR ALA SER GLY ILE SER ALA SEQRES 8 A 398 ILE THR THR THR LEU LEU THR LEU CYS GLN GLN GLY ASP SEQRES 9 A 398 HIS ILE VAL SER ALA SER ALA ILE TYR GLY CYS THR HIS SEQRES 10 A 398 ALA PHE LEU SER HIS SER MET PRO LYS PHE GLY ILE ASN SEQRES 11 A 398 VAL SER PHE VAL ASP ALA ALA LYS PRO GLU GLU ILE ARG SEQRES 12 A 398 ALA ALA MET ARG PRO GLU THR LYS VAL VAL TYR ILE GLU SEQRES 13 A 398 THR PRO ALA ASN PRO THR LEU SER LEU VAL ASP ILE GLU SEQRES 14 A 398 THR VAL ALA GLY ILE ALA HIS GLN GLN GLY ALA LEU LEU SEQRES 15 A 398 VAL VAL ASP ASN THR PHE MET SER PRO TYR CYS GLN GLN SEQRES 16 A 398 PRO LEU GLN LEU GLY ALA ASP ILE VAL VAL HIS SER VAL SEQRES 17 A 398 THR LYS TYR ILE ASN GLY HIS GLY ASP VAL ILE GLY GLY SEQRES 18 A 398 ILE ILE VAL GLY LYS GLN GLU PHE ILE ASP GLN ALA ARG SEQRES 19 A 398 PHE VAL GLY LEU LYS ASP ILE THR GLY GLY CYS MET SER SEQRES 20 A 398 PRO PHE ASN ALA TRP LEU THR LEU ARG GLY VAL LYS THR SEQRES 21 A 398 LEU GLY ILE ARG MET GLU ARG HIS CYS GLU ASN ALA LEU SEQRES 22 A 398 LYS ILE ALA ARG PHE LEU GLU GLY HIS PRO SER ILE THR SEQRES 23 A 398 ARG VAL TYR TYR PRO GLY LEU SER SER HIS PRO GLN TYR SEQRES 24 A 398 GLU LEU GLY GLN ARG GLN MET SER LEU PRO GLY GLY ILE SEQRES 25 A 398 ILE SER PHE GLU ILE ALA GLY GLY LEU GLU ALA GLY ARG SEQRES 26 A 398 ARG MET ILE ASN SER VAL GLU LEU CYS LEU LEU ALA VAL SEQRES 27 A 398 SER LEU GLY ASP THR GLU THR LEU ILE GLN HIS PRO ALA SEQRES 28 A 398 SER MET THR HIS SER PRO VAL ALA PRO GLU GLU ARG LEU SEQRES 29 A 398 LYS ALA GLY ILE THR ASP GLY LEU ILE ARG LEU SER VAL SEQRES 30 A 398 GLY LEU GLU ASP PRO GLU ASP ILE ILE ASN ASP LEU GLU SEQRES 31 A 398 HIS ALA ILE ARG LYS ALA THR PHE HET LCS A 401 22 HET PGE A 402 10 HET PGE A 403 10 HET PEG A 404 7 HET PEG A 405 7 HET CL A 406 1 HETNAM LCS [5-HYDROXY-6-METHYL-4-({[(4E)-3-OXO-1,2-OXAZOLIDIN-4- HETNAM 2 LCS YLIDENE]AMINO}METHYL)PYRIDIN-3-YL]METHYL DIHYDROGEN HETNAM 3 LCS PHOSPHATE HETNAM PGE TRIETHYLENE GLYCOL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM CL CHLORIDE ION FORMUL 2 LCS C11 H14 N3 O7 P FORMUL 3 PGE 2(C6 H14 O4) FORMUL 5 PEG 2(C4 H10 O3) FORMUL 7 CL CL 1- FORMUL 8 HOH *266(H2 O) HELIX 1 1 ASP A 3 TYR A 7 5 5 HELIX 2 2 GLY A 8 ALA A 16 1 9 HELIX 3 3 SER A 41 ALA A 50 1 10 HELIX 4 4 ASN A 63 ARG A 78 1 16 HELIX 5 5 SER A 87 CYS A 100 1 14 HELIX 6 6 TYR A 113 SER A 123 1 11 HELIX 7 7 MET A 124 GLY A 128 5 5 HELIX 8 8 LYS A 138 MET A 146 1 9 HELIX 9 9 ASP A 167 GLN A 178 1 12 HELIX 10 10 GLN A 195 GLY A 200 5 6 HELIX 11 11 LYS A 226 VAL A 236 1 11 HELIX 12 12 VAL A 236 ILE A 241 1 6 HELIX 13 13 SER A 247 LYS A 259 1 13 HELIX 14 14 THR A 260 GLY A 281 1 22 HELIX 15 15 GLN A 298 MET A 306 1 9 HELIX 16 16 GLY A 319 ASN A 329 1 11 HELIX 17 17 ALA A 359 ALA A 366 1 8 HELIX 18 18 ASP A 381 THR A 397 1 17 SHEET 1 A 7 ALA A 81 THR A 85 0 SHEET 2 A 7 GLY A 221 GLY A 225 -1 O GLY A 221 N THR A 85 SHEET 3 A 7 ILE A 203 SER A 207 -1 N VAL A 204 O VAL A 224 SHEET 4 A 7 LEU A 181 ASP A 185 1 N VAL A 184 O VAL A 205 SHEET 5 A 7 THR A 150 GLU A 156 1 N VAL A 153 O VAL A 183 SHEET 6 A 7 HIS A 105 ALA A 109 1 N VAL A 107 O TYR A 154 SHEET 7 A 7 ASN A 130 VAL A 134 1 O SER A 132 N ILE A 106 SHEET 1 B 5 ILE A 285 TYR A 289 0 SHEET 2 B 5 ILE A 312 ILE A 317 -1 O SER A 314 N TYR A 289 SHEET 3 B 5 LEU A 372 SER A 376 -1 O LEU A 375 N ILE A 313 SHEET 4 B 5 LEU A 346 GLN A 348 -1 N LEU A 346 O SER A 376 SHEET 5 B 5 LEU A 335 LEU A 336 1 N LEU A 335 O ILE A 347 CISPEP 1 THR A 157 PRO A 158 0 -10.23 SITE 1 AC1 16 TYR A 58 ARG A 60 SER A 87 GLY A 88 SITE 2 AC1 16 ILE A 89 TYR A 113 ASP A 185 THR A 187 SITE 3 AC1 16 SER A 207 THR A 209 LYS A 210 VAL A 338 SITE 4 AC1 16 SER A 339 LEU A 340 ARG A 374 HOH A 685 SITE 1 AC2 6 PRO A 191 TYR A 192 GLN A 303 GLN A 305 SITE 2 AC2 6 SER A 307 HOH A 676 SITE 1 AC3 4 GLU A 270 LYS A 274 GLU A 383 HOH A 627 SITE 1 AC4 6 ARG A 277 GLU A 280 GLY A 292 LEU A 293 SITE 2 AC4 6 SER A 294 SER A 295 SITE 1 AC5 6 PHE A 9 TYR A 192 GLU A 266 SER A 307 SITE 2 AC5 6 HOH A 665 HOH A 745 SITE 1 AC6 4 ASN A 271 GLY A 378 GLU A 380 ILE A 385 CRYST1 56.270 122.890 126.610 90.00 90.00 90.00 I 2 2 2 8 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 0.017771 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008137 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007898 0.00000