HEADER LIGASE/PRODUCT 01-JUN-12 4FFM TITLE PYLC IN COMPLEX WITH L-LYSINE-NE-D-ORNITHINE (COCRYSTALLIZED WITH L- TITLE 2 LYSINE-NE-D-ORNITHINE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYLC; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOSARCINA BARKERI; SOURCE 3 ORGANISM_TAXID: 269797; SOURCE 4 STRAIN: FUSARO; SOURCE 5 GENE: MBAR_A0837; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PET28B KEYWDS AMINO ACID, BIOSYNTHESIS OF PYRROLYSINE, ISOPEPTIDE BOND FORMATION, KEYWDS 2 ATP-GRASP FOLD, LIGASE, ATP-BINDING, L-LYSINE AND 3R-METHYL-D- KEYWDS 3 ORNITHINE, CYTOSOL, LIGASE-PRODUCT COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR F.QUITTERER,A.LIST,P.BECK,A.BACHER,M.GROLL REVDAT 4 28-FEB-24 4FFM 1 REMARK LINK REVDAT 3 26-FEB-20 4FFM 1 REMARK REVDAT 2 27-MAR-13 4FFM 1 JRNL REVDAT 1 19-SEP-12 4FFM 0 JRNL AUTH F.QUITTERER,A.LIST,P.BECK,A.BACHER,M.GROLL JRNL TITL BIOSYNTHESIS OF THE 22ND GENETICALLY ENCODED AMINO ACID JRNL TITL 2 PYRROLYSINE: STRUCTURE AND REACTION MECHANISM OF PYLC AT JRNL TITL 3 1.5A RESOLUTION. JRNL REF J.MOL.BIOL. V. 424 270 2012 JRNL REFN ISSN 0022-2836 JRNL PMID 22985965 JRNL DOI 10.1016/J.JMB.2012.09.007 REMARK 2 REMARK 2 RESOLUTION. 1.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 25744 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1355 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) : 1.91 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1584 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.58 REMARK 3 BIN R VALUE (WORKING SET) : 0.2190 REMARK 3 BIN FREE R VALUE SET COUNT : 86 REMARK 3 BIN FREE R VALUE : 0.2700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2733 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 78 REMARK 3 SOLVENT ATOMS : 230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.51000 REMARK 3 B22 (A**2) : 1.51000 REMARK 3 B33 (A**2) : -3.01000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.137 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.100 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.739 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2884 ; 0.011 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3888 ; 1.673 ; 2.017 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 340 ; 5.591 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 123 ;40.129 ;24.390 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 498 ;16.181 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;12.754 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 429 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2110 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 2884 ; 2.249 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 55 ;30.817 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2986 ;12.182 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 363 REMARK 3 RESIDUE RANGE : A 901 A 905 REMARK 3 ORIGIN FOR THE GROUP (A): 14.8080 4.9840 26.1030 REMARK 3 T TENSOR REMARK 3 T11: 0.0165 T22: 0.0075 REMARK 3 T33: 0.0032 T12: -0.0021 REMARK 3 T13: -0.0036 T23: 0.0021 REMARK 3 L TENSOR REMARK 3 L11: 0.0876 L22: 0.1326 REMARK 3 L33: 0.1061 L12: 0.0077 REMARK 3 L13: 0.0118 L23: 0.0255 REMARK 3 S TENSOR REMARK 3 S11: -0.0165 S12: 0.0053 S13: -0.0066 REMARK 3 S21: 0.0050 S22: 0.0248 S23: 0.0079 REMARK 3 S31: 0.0211 S32: 0.0133 S33: -0.0083 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4FFM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1000072840. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-FEB-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : LN2 COOLED FIXED-EXIT SI(111) REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27100 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.63300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES; 200MM MGCL2, 25% PEG4000, PH REMARK 280 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 86.35000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.96000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.96000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 129.52500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.96000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.96000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 43.17500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.96000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.96000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 129.52500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.96000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.96000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 43.17500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 86.35000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 132 REMARK 465 PRO A 133 REMARK 465 CYS A 134 REMARK 465 GLU A 135 REMARK 465 SER A 136 REMARK 465 SER A 137 REMARK 465 SER A 138 REMARK 465 VAL A 139 REMARK 465 GLY A 140 REMARK 465 ASP A 146 REMARK 465 ASP A 147 REMARK 465 LYS A 148 REMARK 465 ASP A 149 REMARK 465 LEU A 150 REMARK 465 GLU A 151 REMARK 465 ARG A 276 REMARK 465 ALA A 277 REMARK 465 ILE A 278 REMARK 465 PRO A 279 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 ASP A 241 CB - CG - OD2 ANGL. DEV. = 7.2 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 LYS A 10 -128.96 -106.94 REMARK 500 ARG A 122 69.71 29.54 REMARK 500 VAL A 182 -97.86 -95.09 REMARK 500 GLN A 247 -64.35 76.58 REMARK 500 THR A 269 -87.80 -112.43 REMARK 500 GLU A 293 119.13 -39.87 REMARK 500 GLU A 328 94.23 -69.13 REMARK 500 TYR A 329 120.28 75.01 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 MG A 903 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 227 OE1 REMARK 620 2 GLU A 239 OE2 73.0 REMARK 620 3 ADP A 902 O3A 153.0 107.1 REMARK 620 4 ADP A 902 O1A 86.1 120.5 70.4 REMARK 620 5 ADP A 902 O1B 139.8 105.2 67.1 124.4 REMARK 620 6 HOH A1160 O 66.9 136.5 116.2 73.6 95.0 REMARK 620 7 HOH A1204 O 67.3 77.7 139.7 142.5 73.0 71.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 904 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 239 OE2 REMARK 620 2 GLU A 239 OE1 73.3 REMARK 620 3 ASP A 241 OD2 89.0 84.1 REMARK 620 4 ADP A 902 O1B 77.6 129.4 135.9 REMARK 620 5 ADP A 902 O3B 102.7 79.7 156.3 67.5 REMARK 620 6 HOH A1192 O 158.5 87.0 80.4 122.7 81.5 REMARK 620 7 HOH A1226 O 119.2 162.3 83.7 67.8 107.4 78.3 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0TF A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 905 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2YZG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF D-ALA:D-ALA LIGASE FROM THERMUS THERMOPHILUS REMARK 900 HB8 REMARK 900 RELATED ID: 3OUZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE-ADP COMPLEX FROM REMARK 900 CAMPYLOBACTER JEJUNI REMARK 900 RELATED ID: 4FFL RELATED DB: PDB REMARK 900 RELATED ID: 4FFN RELATED DB: PDB REMARK 900 RELATED ID: 4FFO RELATED DB: PDB REMARK 900 RELATED ID: 4FFP RELATED DB: PDB REMARK 900 RELATED ID: 4FFR RELATED DB: PDB DBREF 4FFM A 1 363 UNP Q46E79 Q46E79_METBF 1 363 SEQRES 1 A 363 MET LYS THR ILE CYS LEU VAL GLY GLY LYS LEU GLN GLY SEQRES 2 A 363 PHE GLU ALA ALA TYR LEU SER LYS LYS ALA GLY MET LYS SEQRES 3 A 363 VAL VAL LEU VAL ASP LYS ASN PRO GLN ALA LEU ILE ARG SEQRES 4 A 363 ASN TYR ALA ASP GLU PHE TYR CYS PHE ASP VAL ILE LYS SEQRES 5 A 363 GLU PRO GLU LYS LEU LEU GLU LEU SER LYS ARG VAL ASP SEQRES 6 A 363 ALA VAL LEU PRO VAL ASN GLU ASN LEU ALA CYS ILE GLU SEQRES 7 A 363 PHE LEU ASN SER ILE LYS GLU LYS PHE SER CYS PRO VAL SEQRES 8 A 363 LEU PHE ASP PHE GLU ALA TYR ARG ILE SER ARG ASP LYS SEQRES 9 A 363 LYS LYS SER LYS ASP TYR PHE LYS SER ILE GLY VAL PRO SEQRES 10 A 363 THR PRO GLN ASP ARG PRO SER LYS PRO PRO TYR PHE VAL SEQRES 11 A 363 LYS PRO PRO CYS GLU SER SER SER VAL GLY ALA ARG ILE SEQRES 12 A 363 ILE TYR ASP ASP LYS ASP LEU GLU GLY LEU GLU PRO ASP SEQRES 13 A 363 THR LEU VAL GLU GLU TYR VAL GLU GLY GLU VAL VAL SER SEQRES 14 A 363 LEU GLU VAL VAL GLY ASP GLY SER HIS PHE ALA VAL VAL SEQRES 15 A 363 LYS GLU THR LEU VAL HIS ILE ASP GLU THR TYR ASP CYS SEQRES 16 A 363 HIS MET VAL THR PRO LEU PRO ALA ASN PRO LEU PHE ARG SEQRES 17 A 363 GLN ILE SER HIS ASP LEU ALA ALA ASN LEU PRO LEU LYS SEQRES 18 A 363 GLY ILE MET ASP VAL GLU ALA ILE PHE GLY PRO LYS GLY SEQRES 19 A 363 LEU ARG VAL ILE GLU ILE ASP ALA ARG PHE PRO SER GLN SEQRES 20 A 363 THR PRO THR VAL VAL TYR TYR SER SER GLY ILE ASN LEU SEQRES 21 A 363 ILE GLU LEU LEU PHE ARG ALA PHE THR ASP GLY VAL GLU SEQRES 22 A 363 GLU ILE ARG ALA ILE PRO GLU ASN LYS TYR CYS ILE TYR SEQRES 23 A 363 GLU HIS LEU MET PHE GLY GLU ASN GLY VAL LEU ILE PRO SEQRES 24 A 363 VAL GLY GLU GLN VAL LEU SER MET GLY SER ASP TYR GLY SEQRES 25 A 363 LYS PHE TYR GLU GLU PRO GLY ILE GLU ILE PHE LEU CYS SEQRES 26 A 363 LYS GLY GLU TYR PRO VAL PHE THR MET VAL PHE TRP GLY SEQRES 27 A 363 LYS ASP ARG GLU GLU THR GLY ALA LYS ARG CYS LYS GLY SEQRES 28 A 363 LEU SER VAL LEU LYS GLU ARG PHE GLY ALA VAL LEU HET 0TF A 901 18 HET ADP A 902 27 HET MG A 903 1 HET MG A 904 1 HET ATP A 905 31 HETNAM 0TF N~6~-D-ORNITHYL-L-LYSINE HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE FORMUL 2 0TF C11 H24 N4 O3 FORMUL 3 ADP C10 H15 N5 O10 P2 FORMUL 4 MG 2(MG 2+) FORMUL 6 ATP C10 H16 N5 O13 P3 FORMUL 7 HOH *230(H2 O) HELIX 1 1 LYS A 10 ALA A 23 1 14 HELIX 2 2 GLU A 53 LYS A 62 1 10 HELIX 3 3 ASN A 73 ILE A 83 1 11 HELIX 4 4 LYS A 84 PHE A 87 5 4 HELIX 5 5 ASP A 94 ARG A 102 1 9 HELIX 6 6 ASP A 103 ILE A 114 1 12 HELIX 7 7 ASN A 204 ASN A 217 1 14 HELIX 8 8 GLN A 247 GLY A 257 1 11 HELIX 9 9 ASN A 259 THR A 269 1 11 HELIX 10 10 GLU A 293 GLY A 295 5 3 HELIX 11 11 GLY A 301 SER A 306 1 6 HELIX 12 12 ASP A 340 GLY A 360 1 21 SHEET 1 A 4 GLU A 44 CYS A 47 0 SHEET 2 A 4 LYS A 26 ASP A 31 1 N LEU A 29 O GLU A 44 SHEET 3 A 4 THR A 3 VAL A 7 1 N ILE A 4 O VAL A 28 SHEET 4 A 4 ALA A 66 PRO A 69 1 O LEU A 68 N CYS A 5 SHEET 1 B 3 ARG A 142 ILE A 144 0 SHEET 2 B 3 TYR A 128 LYS A 131 -1 N VAL A 130 O ARG A 142 SHEET 3 B 3 LEU A 158 GLU A 161 -1 O GLU A 160 N PHE A 129 SHEET 1 C 6 PHE A 179 VAL A 181 0 SHEET 2 C 6 GLU A 166 ASP A 175 -1 N VAL A 173 O ALA A 180 SHEET 3 C 6 THR A 185 ILE A 189 -1 O THR A 185 N SER A 169 SHEET 4 C 6 CYS A 195 PRO A 200 -1 O THR A 199 N LEU A 186 SHEET 5 C 6 TYR A 283 PHE A 291 -1 O TYR A 286 N VAL A 198 SHEET 6 C 6 LEU A 297 PRO A 299 -1 O ILE A 298 N MET A 290 SHEET 1 D 9 GLY A 234 ASP A 241 0 SHEET 2 D 9 LYS A 221 GLY A 231 -1 N GLU A 227 O GLU A 239 SHEET 3 D 9 GLU A 166 ASP A 175 -1 N VAL A 168 O ALA A 228 SHEET 4 D 9 THR A 185 ILE A 189 -1 O THR A 185 N SER A 169 SHEET 5 D 9 CYS A 195 PRO A 200 -1 O THR A 199 N LEU A 186 SHEET 6 D 9 TYR A 283 PHE A 291 -1 O TYR A 286 N VAL A 198 SHEET 7 D 9 VAL A 331 GLY A 338 -1 O PHE A 332 N LEU A 289 SHEET 8 D 9 ILE A 320 LYS A 326 -1 N CYS A 325 O VAL A 331 SHEET 9 D 9 ASP A 310 GLU A 317 -1 N PHE A 314 O ILE A 322 LINK OE1 GLU A 227 MG MG A 903 1555 1555 1.98 LINK OE2 GLU A 239 MG MG A 903 1555 1555 1.91 LINK OE2 GLU A 239 MG MG A 904 1555 1555 1.86 LINK OE1 GLU A 239 MG MG A 904 1555 1555 1.92 LINK OD2 ASP A 241 MG MG A 904 1555 1555 1.99 LINK O3A ADP A 902 MG MG A 903 1555 1555 2.67 LINK O1A ADP A 902 MG MG A 903 1555 1555 1.82 LINK O1B ADP A 902 MG MG A 903 1555 1555 1.90 LINK O1B ADP A 902 MG MG A 904 1555 1555 2.83 LINK O3B ADP A 902 MG MG A 904 1555 1555 1.86 LINK MG MG A 903 O HOH A1160 1555 1555 2.82 LINK MG MG A 903 O HOH A1204 1555 1555 2.48 LINK MG MG A 904 O HOH A1192 1555 1555 2.52 LINK MG MG A 904 O HOH A1226 1555 1555 2.09 CISPEP 1 PRO A 126 PRO A 127 0 4.79 CISPEP 2 LEU A 218 PRO A 219 0 -11.82 SITE 1 AC1 16 LYS A 10 LEU A 11 GLN A 12 GLU A 72 SITE 2 AC1 16 SER A 169 GLU A 171 ASP A 225 ARG A 243 SITE 3 AC1 16 PRO A 245 SER A 246 GLN A 247 THR A 248 SITE 4 AC1 16 GLU A 302 ATP A 905 HOH A1001 HOH A1143 SITE 1 AC2 21 LYS A 104 PRO A 119 PHE A 129 LYS A 131 SITE 2 AC2 21 GLU A 160 GLU A 161 TYR A 162 VAL A 163 SITE 3 AC2 21 VAL A 167 ILE A 189 GLU A 227 ILE A 229 SITE 4 AC2 21 GLU A 239 MG A 903 MG A 904 HOH A1011 SITE 5 AC2 21 HOH A1160 HOH A1192 HOH A1195 HOH A1204 SITE 6 AC2 21 HOH A1226 SITE 1 AC3 6 GLU A 227 GLU A 239 ADP A 902 MG A 904 SITE 2 AC3 6 HOH A1160 HOH A1204 SITE 1 AC4 6 GLU A 239 ASP A 241 ADP A 902 MG A 903 SITE 2 AC4 6 HOH A1192 HOH A1226 SITE 1 AC5 16 GLY A 8 LYS A 10 ASP A 31 LYS A 32 SITE 2 AC5 16 PHE A 48 ASP A 49 VAL A 50 ILE A 51 SITE 3 AC5 16 ASN A 71 GLU A 72 ASN A 73 CYS A 76 SITE 4 AC5 16 0TF A 901 HOH A1031 HOH A1088 HOH A1143 CRYST1 61.920 61.920 172.700 90.00 90.00 90.00 P 43 21 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 0.016150 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016150 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005790 0.00000