HEADER LYASE 05-SEP-13 4MKK TITLE CRYSTAL STRUCTURE OF C115A MUTANT L-METHIONINE GAMMA-LYASE FROM TITLE 2 CITROBACTER FREUNDII MODIFIED BY ALLICINE 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; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CITROBACTER FREUNDII; SOURCE 3 ORGANISM_TAXID: 546; SOURCE 4 GENE: 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; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-C115AMGL KEYWDS PYRIDOXAL-5'-PHOSPHATE, PLP-DEPENDENT ENZYME, AMINOTRANSFERASE CLASS- KEYWDS 2 V, LYASE, ALLICINE EXPDTA X-RAY DIFFRACTION AUTHOR S.V.REVTOVICH,A.D.NIKULIN,E.A.MOROZOVA,L.N.ZAKOMIRDINA,T.V.DEMIDKINA REVDAT 4 06-DEC-23 4MKK 1 REMARK REVDAT 3 20-SEP-23 4MKK 1 REMARK SEQADV LINK REVDAT 2 31-DEC-14 4MKK 1 JRNL REVDAT 1 12-NOV-14 4MKK 0 JRNL AUTH E.A.MOROZOVA,S.V.REVTOVICH,N.V.ANUFRIEVA,V.V.KULIKOVA, JRNL AUTH 2 A.D.NIKULIN,T.V.DEMIDKINA JRNL TITL ALLIIN IS A SUICIDE SUBSTRATE OF CITROBACTER FREUNDII JRNL TITL 2 METHIONINE GAMMA-LYASE: STRUCTURAL BASES OF INACTIVATION OF JRNL TITL 3 THE ENZYME. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 70 3034 2014 JRNL REFN ISSN 0907-4449 JRNL PMID 25372692 JRNL DOI 10.1107/S1399004714020938 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 78977 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.138 REMARK 3 FREE R VALUE : 0.173 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 3968 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 33.2049 - 4.3957 0.99 2856 158 0.1447 0.1516 REMARK 3 2 4.3957 - 3.4902 1.00 2820 127 0.1262 0.1678 REMARK 3 3 3.4902 - 3.0493 1.00 2762 143 0.1446 0.1615 REMARK 3 4 3.0493 - 2.7707 1.00 2753 143 0.1443 0.1718 REMARK 3 5 2.7707 - 2.5722 1.00 2714 146 0.1354 0.1761 REMARK 3 6 2.5722 - 2.4206 1.00 2705 165 0.1314 0.1501 REMARK 3 7 2.4206 - 2.2994 1.00 2717 164 0.1246 0.1664 REMARK 3 8 2.2994 - 2.1993 1.00 2697 132 0.1196 0.1506 REMARK 3 9 2.1993 - 2.1147 1.00 2708 140 0.1214 0.1665 REMARK 3 10 2.1147 - 2.0417 1.00 2729 133 0.1288 0.1515 REMARK 3 11 2.0417 - 1.9779 1.00 2695 155 0.1265 0.1879 REMARK 3 12 1.9779 - 1.9213 1.00 2692 153 0.1296 0.1649 REMARK 3 13 1.9213 - 1.8708 1.00 2706 141 0.1303 0.1986 REMARK 3 14 1.8708 - 1.8251 1.00 2687 139 0.1377 0.1808 REMARK 3 15 1.8251 - 1.7836 1.00 2703 136 0.1365 0.1787 REMARK 3 16 1.7836 - 1.7457 1.00 2720 135 0.1377 0.1714 REMARK 3 17 1.7457 - 1.7108 1.00 2679 148 0.1374 0.1924 REMARK 3 18 1.7108 - 1.6785 1.00 2681 155 0.1355 0.2034 REMARK 3 19 1.6785 - 1.6485 1.00 2691 126 0.1414 0.1724 REMARK 3 20 1.6485 - 1.6206 1.00 2676 154 0.1405 0.1942 REMARK 3 21 1.6206 - 1.5944 1.00 2724 123 0.1462 0.1973 REMARK 3 22 1.5944 - 1.5699 1.00 2710 133 0.1547 0.1963 REMARK 3 23 1.5699 - 1.5468 1.00 2660 135 0.1568 0.2040 REMARK 3 24 1.5468 - 1.5250 1.00 2644 155 0.1647 0.2228 REMARK 3 25 1.5250 - 1.5044 0.99 2630 154 0.1829 0.2210 REMARK 3 26 1.5044 - 1.4849 0.99 2654 150 0.1869 0.2258 REMARK 3 27 1.4849 - 1.4663 0.99 2653 141 0.2021 0.2508 REMARK 3 28 1.4663 - 1.4486 0.72 1943 84 0.2336 0.3119 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.38 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 3227 REMARK 3 ANGLE : 1.227 4398 REMARK 3 CHIRALITY : 0.076 502 REMARK 3 PLANARITY : 0.005 573 REMARK 3 DIHEDRAL : 14.531 1236 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4MKK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000082026. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-10 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 : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8943 REMARK 200 MONOCHROMATOR : SI(111), HORIZONTALLY FOCUSSING REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROCESS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 78999 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 4.630 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.03 REMARK 200 R MERGE FOR SHELL (I) : 0.53000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.480 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2RFV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5% MMEPEG 2000, 50MM TRIS-HCL, 0.2MM REMARK 280 PLP, 0.25% DTT, PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 303.0K 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 28.34500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 61.43000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 64.30000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 28.34500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 61.43000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 64.30000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 28.34500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 61.43000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 64.30000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 28.34500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 61.43000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 64.30000 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: 26970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -346.0 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 572 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 748 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 768 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 ALA A 50 REMARK 465 LEU A 51 REMARK 465 GLU A 52 REMARK 465 GLU A 53 REMARK 465 SER A 54 REMARK 465 GLY A 55 REMARK 465 TYR A 56 REMARK 465 ILE A 57 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 NH2 ARG A 60 O HOH A 839 2.02 REMARK 500 O HOH A 729 O HOH A 794 2.05 REMARK 500 O HOH A 741 O HOH A 742 2.07 REMARK 500 O HOH A 628 O HOH A 737 2.12 REMARK 500 NH2 ARG A 60 O HOH A 841 2.17 REMARK 500 O HOH A 650 O HOH A 742 2.17 REMARK 500 O HOH A 750 O HOH A 793 2.17 REMARK 500 O HOH A 780 O HOH A 794 2.18 REMARK 500 OH TYR A 113 O HOH A 788 2.19 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 ARG A 60 30.84 76.21 REMARK 500 SER A 190 160.72 72.42 REMARK 500 LLP A 210 -118.52 -93.79 REMARK 500 ILE A 241 -65.87 -94.01 REMARK 500 VAL A 338 79.73 -108.97 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 ARG A 60 LEU A 61 146.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 408 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PRO A 64 O REMARK 620 2 HOH A 759 O 128.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 409 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 113 OH REMARK 620 2 VAL A 338 O 128.1 REMARK 620 3 HOH A 788 O 98.1 124.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 209 O REMARK 620 2 SER A 339 OG 114.7 REMARK 620 3 ASP A 342 OD1 100.4 108.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 405 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE A 317 O REMARK 620 2 HOH A 582 O 107.3 REMARK 620 3 HOH A 627 O 123.6 119.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 407 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 537 O REMARK 620 2 HOH A 598 O 121.6 REMARK 620 3 HOH A 672 O 107.1 101.6 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE 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 NA A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA 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 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 409 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2RFV RELATED DB: PDB REMARK 900 HIGH RESOLUTION STRUCTURE OF L-METHIONINE GAMMA-LYASE FROM REMARK 900 CITROBACTER FREUNDII (WILD-TYPE) REMARK 900 RELATED ID: 4MKJ RELATED DB: PDB DBREF 4MKK A 1 398 UNP Q84AR1 Q84AR1_CITFR 1 398 SEQADV 4MKK ALA A 115 UNP Q84AR1 CYS 115 ENGINEERED MUTATION SEQADV 4MKK SER A 132 UNP Q84AR1 ARG 132 CONFLICT SEQADV 4MKK PHE A 133 UNP Q84AR1 LEU 133 CONFLICT SEQADV 4MKK ALA A 137 UNP Q84AR1 GLY 137 CONFLICT SEQRES 1 A 398 MET SER ASP C1S 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 ALA 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 LLP 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 C1S 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 MODRES 4MKK C1S A 4 CYS 3-(PROP-2-EN-1-YLDISULFANYL)-L-ALANINE MODRES 4MKK LLP A 210 LYS MODRES 4MKK C1S A 245 CYS 3-(PROP-2-EN-1-YLDISULFANYL)-L-ALANINE HET C1S A 4 10 HET LLP A 210 24 HET C1S A 245 20 HET PGE A 401 10 HET PGE A 402 10 HET NA A 403 1 HET NA A 404 1 HET NA A 405 1 HET CL A 406 1 HET NA A 407 1 HET NA A 408 1 HET K A 409 1 HETNAM C1S 3-(PROP-2-EN-1-YLDISULFANYL)-L-ALANINE HETNAM LLP (2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5- HETNAM 2 LLP (PHOSPHONOOXYMETHYL)PYRIDIN-4- HETNAM 3 LLP YL]METHYLIDENEAMINO]HEXANOIC ACID HETNAM PGE TRIETHYLENE GLYCOL HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM K POTASSIUM ION HETSYN LLP N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE FORMUL 1 C1S 2(C6 H11 N O2 S2) FORMUL 1 LLP C14 H22 N3 O7 P FORMUL 2 PGE 2(C6 H14 O4) FORMUL 4 NA 5(NA 1+) FORMUL 7 CL CL 1- FORMUL 10 K K 1+ FORMUL 11 HOH *342(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 PHE A 49 1 9 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 HIS A 122 1 10 HELIX 7 7 HIS A 122 PHE A 127 1 6 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 HIS A 349 THR A 354 1 6 HELIX 18 18 ALA A 359 ALA A 366 1 8 HELIX 19 19 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 ILE A 203 SHEET 5 A 7 THR A 150 GLU A 156 1 N VAL A 153 O LEU A 181 SHEET 6 A 7 HIS A 105 ALA A 109 1 N HIS A 105 O LYS A 151 SHEET 7 A 7 ASN A 130 VAL A 134 1 O SER A 132 N SER A 108 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 LINK C ASP A 3 N C1S A 4 1555 1555 1.33 LINK C C1S A 4 N ARG A 5 1555 1555 1.33 LINK C THR A 209 N LLP A 210 1555 1555 1.33 LINK C LLP A 210 N TYR A 211 1555 1555 1.33 LINK C GLY A 244 N AC1S A 245 1555 1555 1.32 LINK C GLY A 244 N BC1S A 245 1555 1555 1.33 LINK C AC1S A 245 N MET A 246 1555 1555 1.33 LINK C BC1S A 245 N MET A 246 1555 1555 1.33 LINK O PRO A 64 NA NA A 408 1555 1555 2.70 LINK O ALA A 84 NA NA A 404 1555 1555 2.75 LINK OH BTYR A 113 K K A 409 1555 1555 2.45 LINK O THR A 209 NA NA A 403 1555 1555 2.89 LINK O ILE A 317 NA NA A 405 1555 1555 2.63 LINK O AVAL A 338 K K A 409 1555 1555 2.67 LINK OG BSER A 339 NA NA A 403 1555 1555 2.87 LINK OD1 ASP A 342 NA NA A 403 1555 1555 2.68 LINK NA NA A 405 O HOH A 582 1555 1555 2.75 LINK NA NA A 405 O HOH A 627 1555 1555 2.78 LINK NA NA A 407 O HOH A 537 1555 1555 2.86 LINK NA NA A 407 O HOH A 598 1555 1555 2.76 LINK NA NA A 407 O HOH A 672 1555 1555 2.78 LINK NA NA A 408 O HOH A 759 1555 1555 2.71 LINK K K A 409 O HOH A 788 1555 1555 3.28 CISPEP 1 THR A 157 PRO A 158 0 -7.14 CISPEP 2 ASN A 160 PRO A 161 0 -3.63 SITE 1 AC1 8 PRO A 191 TYR A 192 CYS A 193 GLN A 195 SITE 2 AC1 8 GLN A 303 SER A 307 HOH A 751 HOH A 827 SITE 1 AC2 4 GLU A 270 LYS A 274 PRO A 382 GLU A 383 SITE 1 AC3 5 SER A 35 THR A 36 THR A 209 SER A 339 SITE 2 AC3 5 ASP A 342 SITE 1 AC4 3 ALA A 84 C1S A 245 MET A 246 SITE 1 AC5 5 ILE A 317 GLY A 319 GLY A 320 HOH A 582 SITE 2 AC5 5 HOH A 627 SITE 1 AC6 4 ARG A 267 LEU A 379 GLU A 380 NA A 407 SITE 1 AC7 5 PRO A 382 CL A 406 HOH A 537 HOH A 598 SITE 2 AC7 5 HOH A 672 SITE 1 AC8 3 PRO A 64 ASP A 67 HOH A 759 SITE 1 AC9 2 TYR A 113 VAL A 338 CRYST1 56.690 122.860 128.600 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 0.017640 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008140 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007776 0.00000