HEADER LYASE 07-JUL-20 7CIM TITLE CRYSTAL STRUCTURE OF L-METHIONINE DECARBOXYLASE FROM STREPTOMYCES TITLE 2 SP.590 IN COMPLEXED WITH 3-METHLYTHIOPROPYLAMINE (GEMINAL DIAMINE TITLE 3 FORM). COMPND MOL_ID: 1; COMPND 2 MOLECULE: L-METHIONINE DECARBOXYLASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 4.1.1.57; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES SP. 590 KI-2014; SOURCE 3 ORGANISM_TAXID: 1510823; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET-52B KEYWDS DECARBOXYLASE, PLP-DEPENDENT ENZYMES, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR A.OKAWA,T.SHIBA,M.HAYASHI,Y.ONOUE,M.MUROTA,D.SATO,J.INAGAKI,T.TAMURA, AUTHOR 2 S.HARADA,K.INAGAKI REVDAT 3 29-NOV-23 7CIM 1 REMARK REVDAT 2 03-MAR-21 7CIM 1 JRNL REVDAT 1 27-JAN-21 7CIM 0 JRNL AUTH A.OKAWA,T.SHIBA,M.HAYASHI,Y.ONOUE,M.MUROTA,D.SATO,J.INAGAKI, JRNL AUTH 2 T.TAMURA,S.HARADA,K.INAGAKI JRNL TITL STRUCTURAL BASIS FOR SUBSTRATE SPECIFICITY OF L-METHIONINE JRNL TITL 2 DECARBOXYLASE. JRNL REF PROTEIN SCI. V. 30 663 2021 JRNL REFN ESSN 1469-896X JRNL PMID 33452696 JRNL DOI 10.1002/PRO.4027 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 85096 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4496 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6026 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.38 REMARK 3 BIN R VALUE (WORKING SET) : 0.3810 REMARK 3 BIN FREE R VALUE SET COUNT : 342 REMARK 3 BIN FREE R VALUE : 0.3660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8160 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 271 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.92 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.151 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.138 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.118 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.007 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8455 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 7800 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11522 ; 1.460 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): 17950 ; 1.009 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 1040 ; 6.557 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 397 ;33.352 ;22.947 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1267 ;14.587 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 72 ;13.495 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1207 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 9640 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1982 ; 0.002 ; 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): 4171 ; 2.173 ; 3.469 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 4169 ; 2.170 ; 3.467 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5206 ; 3.554 ; 5.182 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 5207 ; 3.554 ; 5.184 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 4284 ; 2.419 ; 3.722 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 4285 ; 2.419 ; 3.722 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 6317 ; 3.945 ; 5.500 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 9631 ; 6.118 ;27.295 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 9572 ; 6.117 ;27.277 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 : 1.20 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 7CIM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1300017679. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6-6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.90000 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 88135 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.41900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: 7CIF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MMT BUFFER PH 6.0, 23.5 % (W/V) REMARK 280 PEG1500, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 62.81950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 73.90650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 62.81950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 73.90650 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 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: 9420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -61.0 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 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 SER A 2 REMARK 465 PRO A 3 REMARK 465 THR A 4 REMARK 465 ALA A 5 REMARK 465 PHE A 6 REMARK 465 PRO A 7 REMARK 465 ALA A 8 REMARK 465 ALA A 9 REMARK 465 GLU A 10 REMARK 465 THR A 11 REMARK 465 ALA A 12 REMARK 465 THR A 13 REMARK 465 ALA A 14 REMARK 465 PRO A 15 REMARK 465 ALA A 16 REMARK 465 THR A 17 REMARK 465 PRO A 162 REMARK 465 THR A 163 REMARK 465 ALA A 164 REMARK 465 PRO A 165 REMARK 465 PHE A 166 REMARK 465 ASP A 167 REMARK 465 ALA A 168 REMARK 465 VAL A 169 REMARK 465 ARG A 170 REMARK 465 TYR A 171 REMARK 465 VAL A 172 REMARK 465 LYS A 173 REMARK 465 ALA A 174 REMARK 465 ASP A 175 REMARK 465 ALA A 556 REMARK 465 PRO A 557 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 PRO B 3 REMARK 465 THR B 4 REMARK 465 ALA B 5 REMARK 465 PHE B 6 REMARK 465 PRO B 7 REMARK 465 ALA B 8 REMARK 465 ALA B 9 REMARK 465 GLU B 10 REMARK 465 THR B 11 REMARK 465 ALA B 12 REMARK 465 THR B 13 REMARK 465 ALA B 14 REMARK 465 PRO B 15 REMARK 465 ALA B 16 REMARK 465 THR B 17 REMARK 465 ALA B 18 REMARK 465 VAL B 19 REMARK 465 ASP B 20 REMARK 465 PRO B 21 REMARK 465 GLY B 22 REMARK 465 PRO B 23 REMARK 465 THR B 163 REMARK 465 ALA B 164 REMARK 465 PRO B 165 REMARK 465 PHE B 166 REMARK 465 ASP B 167 REMARK 465 ALA B 168 REMARK 465 VAL B 169 REMARK 465 ARG B 170 REMARK 465 TYR B 171 REMARK 465 VAL B 172 REMARK 465 LYS B 173 REMARK 465 ALA B 174 REMARK 465 ASP B 175 REMARK 465 PRO B 176 REMARK 465 ASP B 177 REMARK 465 ARG B 178 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU B 477 CG CD OE1 OE2 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 NZ LYS A 394 C4 G0F A 601 2.18 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 MET A 69 -67.68 -123.74 REMARK 500 GLN A 70 -60.05 67.25 REMARK 500 LEU A 87 126.79 -31.60 REMARK 500 GLN A 160 -124.92 51.50 REMARK 500 ARG A 179 -81.08 63.92 REMARK 500 ASN A 180 100.19 -28.71 REMARK 500 GLN A 319 -87.21 -155.69 REMARK 500 THR A 320 -58.61 -125.41 REMARK 500 LEU A 339 -60.14 -92.76 REMARK 500 PHE A 368 -3.59 -141.39 REMARK 500 ASP A 369 -166.77 -108.82 REMARK 500 LYS A 394 -93.59 -88.29 REMARK 500 THR A 407 -156.68 -151.84 REMARK 500 ILE A 422 65.12 119.74 REMARK 500 MET B 69 58.13 -156.80 REMARK 500 ASN B 86 32.43 -97.52 REMARK 500 LEU B 87 128.62 -36.49 REMARK 500 THR B 320 126.19 -30.67 REMARK 500 ASP B 369 -164.27 -113.70 REMARK 500 LYS B 394 -93.23 -88.49 REMARK 500 THR B 407 -153.24 -145.26 REMARK 500 PRO B 419 94.44 -65.38 REMARK 500 PRO B 425 72.90 -63.95 REMARK 500 PRO B 498 -167.43 -78.04 REMARK 500 ALA B 556 -161.62 69.89 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 PRO B 425 ASP B 426 -142.63 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 A 832 DISTANCE = 7.13 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue G0F A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide G0F B 601 and LYS B REMARK 800 394 DBREF1 7CIM A 1 557 UNP A0A0G4DBU7_9ACTN DBREF2 7CIM A A0A0G4DBU7 1 557 DBREF1 7CIM B 1 557 UNP A0A0G4DBU7_9ACTN DBREF2 7CIM B A0A0G4DBU7 1 557 SEQRES 1 A 557 MET SER PRO THR ALA PHE PRO ALA ALA GLU THR ALA THR SEQRES 2 A 557 ALA PRO ALA THR ALA VAL ASP PRO GLY PRO GLU LEU ASP SEQRES 3 A 557 GLY GLY ASP PHE ALA LEU PRO GLU GLY GLY LEU ASP ASP SEQRES 4 A 557 ASP ARG ARG LEU ARG ALA LEU ASP ALA VAL ASP GLU TYR SEQRES 5 A 557 LEU THR ARG LYS ARG LYS HIS LEU VAL GLY TYR GLN ALA SEQRES 6 A 557 THR GLN ASP MET GLN GLY THR ALA LEU ASP LEU ALA ARG SEQRES 7 A 557 PHE MET PRO ASN ASN ILE ASN ASN LEU GLY ASP PRO PHE SEQRES 8 A 557 GLN SER GLY GLY TYR LYS PRO ASN THR LYS VAL VAL GLU SEQRES 9 A 557 ARG ALA VAL LEU ASP TYR TYR ALA LYS LEU TRP HIS ALA SEQRES 10 A 557 GLU ARG PRO HIS ASP PRO ALA ASP PRO GLU SER TYR TRP SEQRES 11 A 557 GLY TYR MET LEU SER MET GLY SER THR GLU GLY ASN MET SEQRES 12 A 557 TYR ALA LEU TRP ASN ALA ARG ASP TYR LEU SER GLY LYS SEQRES 13 A 557 ALA LEU ILE GLN PRO PRO THR ALA PRO PHE ASP ALA VAL SEQRES 14 A 557 ARG TYR VAL LYS ALA ASP PRO ASP ARG ARG ASN PRO ASN SEQRES 15 A 557 ALA HIS HIS PRO VAL ALA PHE TYR SER GLU ASP THR HIS SEQRES 16 A 557 TYR SER PHE ALA LYS ALA VAL ALA VAL LEU GLY VAL GLU SEQRES 17 A 557 THR PHE HIS ALA VAL GLY LEU GLU LYS TYR ALA ASP GLU SEQRES 18 A 557 CYS PRO LEU VAL ASP PRO VAL THR GLY LEU ARG THR TRP SEQRES 19 A 557 PRO THR GLU VAL PRO SER ARG PRO GLY PRO SER GLY LEU SEQRES 20 A 557 SER TRP ASP GLY PRO GLY GLU ILE ASP VAL ASP ALA LEU SEQRES 21 A 557 ALA VAL LEU VAL GLU PHE PHE ALA ALA LYS GLY HIS PRO SEQRES 22 A 557 VAL PHE VAL ASN LEU ASN LEU GLY SER THR PHE LYS GLY SEQRES 23 A 557 ALA HIS ASP ASP VAL ARG ALA VAL CYS GLU ARG LEU LEU SEQRES 24 A 557 PRO ILE PHE GLU ARG HIS GLY LEU VAL GLN ARG GLU VAL SEQRES 25 A 557 VAL TYR GLY SER CYS PRO GLN THR GLY ARG PRO LEU VAL SEQRES 26 A 557 ASP VAL ARG ARG GLY PHE TRP ILE HIS VAL ASP GLY ALA SEQRES 27 A 557 LEU GLY ALA GLY TYR ALA PRO PHE LEU ARG LEU ALA ALA SEQRES 28 A 557 GLU ASP PRO GLU GLY TYR GLY TRP THR PRO GLU ALA GLU SEQRES 29 A 557 LEU PRO GLU PHE ASP PHE GLY LEU ARG LEU PRO THR ALA SEQRES 30 A 557 GLY HIS GLY GLU VAL ASP MET VAL SER SER ILE ALA MET SEQRES 31 A 557 SER GLY HIS LYS TRP ALA GLY ALA PRO TRP PRO CYS GLY SEQRES 32 A 557 ILE TYR MET THR LYS VAL LYS TYR GLN ILE SER PRO PRO SEQRES 33 A 557 SER GLN PRO ASP TYR ILE GLY ALA PRO ASP THR THR PHE SEQRES 34 A 557 ALA GLY SER ARG ASN GLY PHE SER PRO LEU ILE LEU TRP SEQRES 35 A 557 ASP HIS LEU SER ARG TYR SER TYR ARG ASP GLN VAL GLU SEQRES 36 A 557 ARG ILE ARG GLU ALA GLN GLU LEU ALA ALA TYR LEU GLU SEQRES 37 A 557 ARG ARG LEU THR ALA MET GLU ARG GLU LEU GLY VAL GLU SEQRES 38 A 557 LEU TRP PRO ALA ARG THR PRO GLY ALA VAL THR VAL ARG SEQRES 39 A 557 PHE ARG LYS PRO SER ALA GLU LEU VAL ALA LYS TRP SER SEQRES 40 A 557 LEU SER SER GLN ASP VAL LEU MET VAL PRO GLY ASP GLU SEQRES 41 A 557 THR THR ARG ARG SER TYR VAL HIS VAL PHE VAL MET PRO SEQRES 42 A 557 SER VAL ASP ARG ALA LYS LEU ASP ALA LEU LEU ALA GLU SEQRES 43 A 557 LEU ALA GLU ASP PRO VAL ILE LEU GLY ALA PRO SEQRES 1 B 557 MET SER PRO THR ALA PHE PRO ALA ALA GLU THR ALA THR SEQRES 2 B 557 ALA PRO ALA THR ALA VAL ASP PRO GLY PRO GLU LEU ASP SEQRES 3 B 557 GLY GLY ASP PHE ALA LEU PRO GLU GLY GLY LEU ASP ASP SEQRES 4 B 557 ASP ARG ARG LEU ARG ALA LEU ASP ALA VAL ASP GLU TYR SEQRES 5 B 557 LEU THR ARG LYS ARG LYS HIS LEU VAL GLY TYR GLN ALA SEQRES 6 B 557 THR GLN ASP MET GLN GLY THR ALA LEU ASP LEU ALA ARG SEQRES 7 B 557 PHE MET PRO ASN ASN ILE ASN ASN LEU GLY ASP PRO PHE SEQRES 8 B 557 GLN SER GLY GLY TYR LYS PRO ASN THR LYS VAL VAL GLU SEQRES 9 B 557 ARG ALA VAL LEU ASP TYR TYR ALA LYS LEU TRP HIS ALA SEQRES 10 B 557 GLU ARG PRO HIS ASP PRO ALA ASP PRO GLU SER TYR TRP SEQRES 11 B 557 GLY TYR MET LEU SER MET GLY SER THR GLU GLY ASN MET SEQRES 12 B 557 TYR ALA LEU TRP ASN ALA ARG ASP TYR LEU SER GLY LYS SEQRES 13 B 557 ALA LEU ILE GLN PRO PRO THR ALA PRO PHE ASP ALA VAL SEQRES 14 B 557 ARG TYR VAL LYS ALA ASP PRO ASP ARG ARG ASN PRO ASN SEQRES 15 B 557 ALA HIS HIS PRO VAL ALA PHE TYR SER GLU ASP THR HIS SEQRES 16 B 557 TYR SER PHE ALA LYS ALA VAL ALA VAL LEU GLY VAL GLU SEQRES 17 B 557 THR PHE HIS ALA VAL GLY LEU GLU LYS TYR ALA ASP GLU SEQRES 18 B 557 CYS PRO LEU VAL ASP PRO VAL THR GLY LEU ARG THR TRP SEQRES 19 B 557 PRO THR GLU VAL PRO SER ARG PRO GLY PRO SER GLY LEU SEQRES 20 B 557 SER TRP ASP GLY PRO GLY GLU ILE ASP VAL ASP ALA LEU SEQRES 21 B 557 ALA VAL LEU VAL GLU PHE PHE ALA ALA LYS GLY HIS PRO SEQRES 22 B 557 VAL PHE VAL ASN LEU ASN LEU GLY SER THR PHE LYS GLY SEQRES 23 B 557 ALA HIS ASP ASP VAL ARG ALA VAL CYS GLU ARG LEU LEU SEQRES 24 B 557 PRO ILE PHE GLU ARG HIS GLY LEU VAL GLN ARG GLU VAL SEQRES 25 B 557 VAL TYR GLY SER CYS PRO GLN THR GLY ARG PRO LEU VAL SEQRES 26 B 557 ASP VAL ARG ARG GLY PHE TRP ILE HIS VAL ASP GLY ALA SEQRES 27 B 557 LEU GLY ALA GLY TYR ALA PRO PHE LEU ARG LEU ALA ALA SEQRES 28 B 557 GLU ASP PRO GLU GLY TYR GLY TRP THR PRO GLU ALA GLU SEQRES 29 B 557 LEU PRO GLU PHE ASP PHE GLY LEU ARG LEU PRO THR ALA SEQRES 30 B 557 GLY HIS GLY GLU VAL ASP MET VAL SER SER ILE ALA MET SEQRES 31 B 557 SER GLY HIS LYS TRP ALA GLY ALA PRO TRP PRO CYS GLY SEQRES 32 B 557 ILE TYR MET THR LYS VAL LYS TYR GLN ILE SER PRO PRO SEQRES 33 B 557 SER GLN PRO ASP TYR ILE GLY ALA PRO ASP THR THR PHE SEQRES 34 B 557 ALA GLY SER ARG ASN GLY PHE SER PRO LEU ILE LEU TRP SEQRES 35 B 557 ASP HIS LEU SER ARG TYR SER TYR ARG ASP GLN VAL GLU SEQRES 36 B 557 ARG ILE ARG GLU ALA GLN GLU LEU ALA ALA TYR LEU GLU SEQRES 37 B 557 ARG ARG LEU THR ALA MET GLU ARG GLU LEU GLY VAL GLU SEQRES 38 B 557 LEU TRP PRO ALA ARG THR PRO GLY ALA VAL THR VAL ARG SEQRES 39 B 557 PHE ARG LYS PRO SER ALA GLU LEU VAL ALA LYS TRP SER SEQRES 40 B 557 LEU SER SER GLN ASP VAL LEU MET VAL PRO GLY ASP GLU SEQRES 41 B 557 THR THR ARG ARG SER TYR VAL HIS VAL PHE VAL MET PRO SEQRES 42 B 557 SER VAL ASP ARG ALA LYS LEU ASP ALA LEU LEU ALA GLU SEQRES 43 B 557 LEU ALA GLU ASP PRO VAL ILE LEU GLY ALA PRO HET G0F A 601 21 HET G0F B 601 21 HETNAM G0F [6-METHYL-4-[(3-METHYLSULFANYLPROPYLAMINO)METHYL]-5- HETNAM 2 G0F OXIDANYL-PYRIDIN-3-YL]METHYL DIHYDROGEN PHOSPHATE FORMUL 3 G0F 2(C12 H21 N2 O5 P S) FORMUL 5 HOH *271(H2 O) HELIX 1 AA1 ASP A 26 PHE A 30 5 5 HELIX 2 AA2 ASP A 38 LEU A 60 1 23 HELIX 3 AA3 GLN A 70 ALA A 77 1 8 HELIX 4 AA4 ARG A 78 MET A 80 5 3 HELIX 5 AA5 THR A 100 TRP A 115 1 16 HELIX 6 AA6 GLY A 137 GLY A 155 1 19 HELIX 7 AA7 HIS A 195 GLY A 206 1 12 HELIX 8 AA8 PHE A 210 TYR A 218 1 9 HELIX 9 AA9 LEU A 247 GLY A 251 5 5 HELIX 10 AB1 ASP A 256 LYS A 270 1 15 HELIX 11 AB2 ASP A 290 HIS A 305 1 16 HELIX 12 AB3 LEU A 339 GLY A 342 5 4 HELIX 13 AB4 TYR A 343 ASP A 353 1 11 HELIX 14 AB5 ASP A 353 GLY A 358 1 6 HELIX 15 AB6 LYS A 410 GLN A 412 5 3 HELIX 16 AB7 PHE A 436 TYR A 448 1 13 HELIX 17 AB8 SER A 449 GLY A 479 1 31 HELIX 18 AB9 SER A 499 SER A 507 1 9 HELIX 19 AC1 ASP A 519 THR A 521 5 3 HELIX 20 AC2 ASP A 536 ALA A 548 1 13 HELIX 21 AC3 ASP A 550 GLY A 555 1 6 HELIX 22 AC4 ASP B 26 ALA B 31 5 6 HELIX 23 AC5 ASP B 38 LEU B 60 1 23 HELIX 24 AC6 MET B 69 ALA B 77 1 9 HELIX 25 AC7 ARG B 78 MET B 80 5 3 HELIX 26 AC8 THR B 100 TRP B 115 1 16 HELIX 27 AC9 GLY B 137 SER B 154 1 18 HELIX 28 AD1 HIS B 195 GLY B 206 1 12 HELIX 29 AD2 PHE B 210 TYR B 218 1 9 HELIX 30 AD3 LEU B 247 GLY B 251 5 5 HELIX 31 AD4 ASP B 256 LYS B 270 1 15 HELIX 32 AD5 ASP B 290 HIS B 305 1 16 HELIX 33 AD6 LEU B 339 GLY B 342 5 4 HELIX 34 AD7 TYR B 343 ASP B 353 1 11 HELIX 35 AD8 ASP B 353 GLY B 358 1 6 HELIX 36 AD9 LYS B 410 GLN B 412 5 3 HELIX 37 AE1 PHE B 436 ARG B 447 1 12 HELIX 38 AE2 SER B 449 GLY B 479 1 31 HELIX 39 AE3 SER B 499 TRP B 506 1 8 HELIX 40 AE4 ASP B 519 THR B 521 5 3 HELIX 41 AE5 ASP B 536 GLU B 549 1 14 HELIX 42 AE6 ASP B 550 GLY B 555 1 6 SHEET 1 AA1 7 TYR A 129 LEU A 134 0 SHEET 2 AA1 7 GLY A 403 LYS A 408 -1 O THR A 407 N TRP A 130 SHEET 3 AA1 7 SER A 387 SER A 391 -1 N MET A 390 O ILE A 404 SHEET 4 AA1 7 PHE A 331 ASP A 336 1 N VAL A 335 O SER A 387 SHEET 5 AA1 7 VAL A 274 ASN A 279 1 N VAL A 276 O HIS A 334 SHEET 6 AA1 7 VAL A 187 PHE A 189 1 N PHE A 189 O PHE A 275 SHEET 7 AA1 7 GLU A 208 THR A 209 1 O GLU A 208 N ALA A 188 SHEET 1 AA2 2 ARG A 310 SER A 316 0 SHEET 2 AA2 2 PRO A 323 ARG A 328 -1 O ASP A 326 N VAL A 312 SHEET 1 AA3 2 ARG A 373 LEU A 374 0 SHEET 2 AA3 2 VAL A 382 ASP A 383 -1 O VAL A 382 N LEU A 374 SHEET 1 AA4 3 THR A 492 ARG A 496 0 SHEET 2 AA4 3 ARG A 523 PHE A 530 -1 O VAL A 527 N PHE A 495 SHEET 3 AA4 3 SER A 509 LEU A 514 -1 N GLN A 511 O TYR A 526 SHEET 1 AA5 7 TYR B 129 LEU B 134 0 SHEET 2 AA5 7 GLY B 403 LYS B 408 -1 O THR B 407 N TRP B 130 SHEET 3 AA5 7 SER B 387 SER B 391 -1 N MET B 390 O ILE B 404 SHEET 4 AA5 7 PHE B 331 ASP B 336 1 N VAL B 335 O SER B 387 SHEET 5 AA5 7 VAL B 274 ASN B 279 1 N VAL B 276 O HIS B 334 SHEET 6 AA5 7 VAL B 187 PHE B 189 1 N VAL B 187 O PHE B 275 SHEET 7 AA5 7 GLU B 208 THR B 209 1 O GLU B 208 N ALA B 188 SHEET 1 AA6 2 ARG B 310 VAL B 313 0 SHEET 2 AA6 2 VAL B 325 ARG B 328 -1 O ARG B 328 N ARG B 310 SHEET 1 AA7 2 ARG B 373 PRO B 375 0 SHEET 2 AA7 2 GLU B 381 ASP B 383 -1 O VAL B 382 N LEU B 374 SHEET 1 AA8 3 THR B 492 ARG B 496 0 SHEET 2 AA8 3 ARG B 523 PHE B 530 -1 O VAL B 527 N PHE B 495 SHEET 3 AA8 3 SER B 509 LEU B 514 -1 N GLN B 511 O TYR B 526 LINK NZ LYS A 394 C4A G0F A 601 1555 1555 1.33 LINK NZ LYS B 394 C4A G0F B 601 1555 1555 1.33 CISPEP 1 ARG A 119 PRO A 120 0 -9.54 CISPEP 2 ARG B 119 PRO B 120 0 -5.49 SITE 1 AC1 15 GLY A 137 SER A 138 THR A 139 ASN A 142 SITE 2 AC1 15 HIS A 195 THR A 283 ASP A 336 ALA A 338 SITE 3 AC1 15 SER A 391 HIS A 393 LYS A 394 HOH A 717 SITE 4 AC1 15 TYR B 421 SER B 432 HOH B 735 SITE 1 AC2 22 SER A 432 HOH A 714 GLN B 64 ALA B 65 SITE 2 AC2 22 THR B 66 GLY B 137 SER B 138 THR B 139 SITE 3 AC2 22 ASN B 142 HIS B 195 GLY B 281 THR B 283 SITE 4 AC2 22 ASP B 336 ALA B 338 SER B 391 GLY B 392 SITE 5 AC2 22 HIS B 393 TRP B 395 ALA B 396 GLY B 397 SITE 6 AC2 22 MET B 532 HOH B 704 CRYST1 125.639 147.813 54.187 90.00 99.47 90.00 C 1 2 1 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 0.007959 0.000000 0.001328 0.00000 SCALE2 0.000000 0.006765 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018710 0.00000