HEADER OXIDOREDUCTASE 06-FEB-13 4J4B TITLE PYLD IN COMPLEX WITH L-LYSINE-NE-D-ORNITHINE AND NADH COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYLD; COMPND 3 CHAIN: A, B; COMPND 4 EC: 1.4.1.-; COMPND 5 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_A0835; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PET28B KEYWDS PYRROLYSINE, 22ND AMINO ACID, BIOSYNTHESIS, ROSSMANN FOLD, KEYWDS 2 DEHYDROGENASE, NADH, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR F.QUITTERER,P.BECK,A.BACHER,M.GROLL REVDAT 3 03-APR-24 4J4B 1 REMARK LINK REVDAT 2 10-JUL-13 4J4B 1 JRNL REVDAT 1 12-JUN-13 4J4B 0 JRNL AUTH F.QUITTERER,P.BECK,A.BACHER,M.GROLL JRNL TITL STRUCTURE AND REACTION MECHANISM OF PYRROLYSINE SYNTHASE JRNL TITL 2 (PYLD). JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 52 7033 2013 JRNL REFN ISSN 1433-7851 JRNL PMID 23720358 JRNL DOI 10.1002/ANIE.201301164 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 43739 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) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2330 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3042 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.89 REMARK 3 BIN R VALUE (WORKING SET) : 0.3060 REMARK 3 BIN FREE R VALUE SET COUNT : 173 REMARK 3 BIN FREE R VALUE : 0.3070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3904 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 128 REMARK 3 SOLVENT ATOMS : 207 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.88 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.14000 REMARK 3 B22 (A**2) : -0.77000 REMARK 3 B33 (A**2) : 0.63000 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): 0.346 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.144 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.109 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.472 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.921 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4115 ; 0.006 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5592 ; 1.203 ; 2.013 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 516 ; 5.249 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 160 ;37.634 ;25.750 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 658 ;15.656 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;12.826 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 652 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3046 ; 0.005 ; 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): 4114 ; 1.562 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 77 ;30.454 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4162 ; 5.708 ; 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 259 REMARK 3 RESIDUE RANGE : A 901 A 903 REMARK 3 RESIDUE RANGE : B 301 B 301 REMARK 3 ORIGIN FOR THE GROUP (A): -17.5201 34.6597 -19.9403 REMARK 3 T TENSOR REMARK 3 T11: 0.1388 T22: 0.0506 REMARK 3 T33: 0.3883 T12: -0.0054 REMARK 3 T13: -0.0898 T23: -0.0560 REMARK 3 L TENSOR REMARK 3 L11: 0.1106 L22: 0.9957 REMARK 3 L33: 1.1977 L12: -0.1377 REMARK 3 L13: 0.1748 L23: 0.0282 REMARK 3 S TENSOR REMARK 3 S11: -0.1141 S12: -0.0130 S13: 0.1877 REMARK 3 S21: 0.2488 S22: -0.1983 S23: -0.0314 REMARK 3 S31: 0.0739 S32: -0.0459 S33: 0.3124 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 259 REMARK 3 RESIDUE RANGE : A 904 A 904 REMARK 3 RESIDUE RANGE : B 302 B 304 REMARK 3 ORIGIN FOR THE GROUP (A): -8.8771 2.4188 -24.8037 REMARK 3 T TENSOR REMARK 3 T11: 0.0298 T22: 0.1244 REMARK 3 T33: 0.0092 T12: 0.0101 REMARK 3 T13: -0.0032 T23: -0.0009 REMARK 3 L TENSOR REMARK 3 L11: 0.2824 L22: 0.3082 REMARK 3 L33: 0.6614 L12: 0.1179 REMARK 3 L13: 0.2656 L23: 0.0036 REMARK 3 S TENSOR REMARK 3 S11: -0.0061 S12: 0.0116 S13: 0.0004 REMARK 3 S21: 0.0729 S22: -0.0103 S23: 0.0052 REMARK 3 S31: -0.0080 S32: 0.0294 S33: 0.0164 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 4J4B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1000077578. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : BRUKER MICROSTAR MICRO-FOCUS REMARK 200 (MONTEL OPTICS) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER PLATINUM 135 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROTEUM PLUS PLUS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46111 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 60.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.7000 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.49600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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: SEMET-MODEL; COORDINATES HAVE NOT BEEN DEPOSITED REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS; 27% PEG3350; 0.2 M LI2SO4, REMARK 280 PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 83.65250 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 83.65250 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 24.19150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 71.22000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 24.19150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 71.22000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 83.65250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 24.19150 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 71.22000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 83.65250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 24.19150 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 71.22000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 39720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -158.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -48.38300 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -83.65250 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 B 425 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 426 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 438 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 444 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 469 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 543 LIES ON A SPECIAL POSITION. 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 A 239 CG CD OE1 OE2 REMARK 470 GLU B 239 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 517 O HOH B 517 3454 1.97 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 ASN A 11 70.00 40.61 REMARK 500 ASN A 62 -12.12 78.90 REMARK 500 ASP A 85 -134.07 60.39 REMARK 500 ASP A 104 -166.71 -101.60 REMARK 500 PRO A 227 -109.89 -86.90 REMARK 500 LEU A 247 -43.57 -155.22 REMARK 500 ASN B 62 -14.93 77.56 REMARK 500 ASP B 85 -137.86 58.74 REMARK 500 ASN B 218 17.77 59.21 REMARK 500 LEU B 247 -39.41 -154.56 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 902 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 202 OE1 REMARK 620 2 GLU A 202 OE2 44.4 REMARK 620 3 THR A 204 O 97.7 76.5 REMARK 620 4 CYS A 206 O 100.5 144.9 116.7 REMARK 620 5 HOH A1001 O 95.1 69.1 113.4 124.4 REMARK 620 N 1 2 3 4 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 245 O REMARK 620 2 NAI A 901 O7N 95.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 303 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 204 O REMARK 620 2 CYS B 206 O 114.3 REMARK 620 3 PRO B 227 O 128.9 93.7 REMARK 620 4 HOH B 407 O 113.8 130.2 65.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 304 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 245 OE2 REMARK 620 2 NAI B 302 O7N 136.4 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAI A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA 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 0TF A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0TF B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAI B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3T7V RELATED DB: PDB REMARK 900 PYLB IN COMPLEX WITH 3R-METHYL-D-ORNITHINE REMARK 900 RELATED ID: 4FFP RELATED DB: PDB REMARK 900 PYLC IN COMPLEX WITH L-LYSINE-NE-D-ORNITHINE REMARK 900 RELATED ID: 4J43 RELATED DB: PDB REMARK 900 RELATED ID: 4J49 RELATED DB: PDB REMARK 900 RELATED ID: 4J4H RELATED DB: PDB DBREF 4J4B A 1 259 UNP Q46E80 Q46E80_METBF 5 263 DBREF 4J4B B 1 259 UNP Q46E80 Q46E80_METBF 5 263 SEQRES 1 A 259 MET ALA LEU LEU THR PRO ASP ASP LEU ILE ASN ILE ASN SEQRES 2 A 259 MET GLN LEU GLN LYS ALA ASP SER ALA VAL GLN GLU VAL SEQRES 3 A 259 THR GLY LEU ASP ILE LYS GLY ILE CYS LYS ALA LEU TYR SEQRES 4 A 259 GLY THR PHE SER SER SER GLU LYS VAL GLY ILE VAL PRO SEQRES 5 A 259 VAL THR SER GLY ASN GLY ILE ILE GLY ASN PHE SER ALA SEQRES 6 A 259 SER LEU HIS ALA ILE THR GLN TYR PHE GLY PHE ASP SER SEQRES 7 A 259 PHE VAL THR ASP MET PRO ASP VAL SER GLY TYR TYR GLU SEQRES 8 A 259 ALA VAL GLN ASN GLY ALA GLU ILE ILE LEU MET ALA ASP SEQRES 9 A 259 ASP ARG THR PHE LEU ALA HIS ASN LEU LYS ASN GLY LYS SEQRES 10 A 259 MET ALA ASN ASN GLN PRO CYS THR GLY ILE ILE TYR ALA SEQRES 11 A 259 GLU ILE ALA SER ARG TYR LEU LYS ALA ASP SER LYS ASP SEQRES 12 A 259 VAL LEU VAL VAL GLY LEU GLY LYS VAL GLY PHE PRO GLY SEQRES 13 A 259 ALA GLU HIS LEU VAL GLN LYS ASP PHE ARG VAL TYR GLY SEQRES 14 A 259 TYR ASP ALA ASP GLU THR LEU LEU GLU ARG ALA THR SER SEQRES 15 A 259 ASN LEU GLY ILE ILE PRO PHE ASP PRO ALA ASN PRO LYS SEQRES 16 A 259 LYS PHE SER ILE ILE PHE GLU ALA THR PRO CYS ALA ASN SEQRES 17 A 259 THR ILE PRO GLU ALA VAL LEU SER GLU ASN CYS VAL LEU SEQRES 18 A 259 SER THR PRO GLY ILE PRO CYS ALA ILE SER GLU GLU LEU SEQRES 19 A 259 ARG ASP LYS TYR GLU VAL GLN LEU ILE ALA GLU PRO LEU SEQRES 20 A 259 GLY ILE GLY THR ALA SER MET LEU TYR SER VAL LEU SEQRES 1 B 259 MET ALA LEU LEU THR PRO ASP ASP LEU ILE ASN ILE ASN SEQRES 2 B 259 MET GLN LEU GLN LYS ALA ASP SER ALA VAL GLN GLU VAL SEQRES 3 B 259 THR GLY LEU ASP ILE LYS GLY ILE CYS LYS ALA LEU TYR SEQRES 4 B 259 GLY THR PHE SER SER SER GLU LYS VAL GLY ILE VAL PRO SEQRES 5 B 259 VAL THR SER GLY ASN GLY ILE ILE GLY ASN PHE SER ALA SEQRES 6 B 259 SER LEU HIS ALA ILE THR GLN TYR PHE GLY PHE ASP SER SEQRES 7 B 259 PHE VAL THR ASP MET PRO ASP VAL SER GLY TYR TYR GLU SEQRES 8 B 259 ALA VAL GLN ASN GLY ALA GLU ILE ILE LEU MET ALA ASP SEQRES 9 B 259 ASP ARG THR PHE LEU ALA HIS ASN LEU LYS ASN GLY LYS SEQRES 10 B 259 MET ALA ASN ASN GLN PRO CYS THR GLY ILE ILE TYR ALA SEQRES 11 B 259 GLU ILE ALA SER ARG TYR LEU LYS ALA ASP SER LYS ASP SEQRES 12 B 259 VAL LEU VAL VAL GLY LEU GLY LYS VAL GLY PHE PRO GLY SEQRES 13 B 259 ALA GLU HIS LEU VAL GLN LYS ASP PHE ARG VAL TYR GLY SEQRES 14 B 259 TYR ASP ALA ASP GLU THR LEU LEU GLU ARG ALA THR SER SEQRES 15 B 259 ASN LEU GLY ILE ILE PRO PHE ASP PRO ALA ASN PRO LYS SEQRES 16 B 259 LYS PHE SER ILE ILE PHE GLU ALA THR PRO CYS ALA ASN SEQRES 17 B 259 THR ILE PRO GLU ALA VAL LEU SER GLU ASN CYS VAL LEU SEQRES 18 B 259 SER THR PRO GLY ILE PRO CYS ALA ILE SER GLU GLU LEU SEQRES 19 B 259 ARG ASP LYS TYR GLU VAL GLN LEU ILE ALA GLU PRO LEU SEQRES 20 B 259 GLY ILE GLY THR ALA SER MET LEU TYR SER VAL LEU HET NAI A 901 44 HET NA A 902 1 HET MG A 903 1 HET 0TF A 904 18 HET 0TF B 301 18 HET NAI B 302 44 HET NA B 303 1 HET MG B 304 1 HETNAM NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE HETNAM NA SODIUM ION HETNAM MG MAGNESIUM ION HETNAM 0TF N~6~-D-ORNITHYL-L-LYSINE HETSYN NAI NADH FORMUL 3 NAI 2(C21 H29 N7 O14 P2) FORMUL 4 NA 2(NA 1+) FORMUL 5 MG 2(MG 2+) FORMUL 6 0TF 2(C11 H24 N4 O3) FORMUL 11 HOH *207(H2 O) HELIX 1 1 THR A 5 ILE A 10 5 6 HELIX 2 2 ASN A 11 GLY A 28 1 18 HELIX 3 3 ASP A 30 GLY A 40 1 11 HELIX 4 4 ASN A 62 PHE A 74 1 13 HELIX 5 5 PRO A 84 ASN A 95 1 12 HELIX 6 6 ASN A 121 ARG A 135 1 15 HELIX 7 7 VAL A 152 LYS A 163 1 12 HELIX 8 8 ASP A 173 GLY A 185 1 13 HELIX 9 9 PRO A 211 ALA A 213 5 3 HELIX 10 10 SER A 231 TYR A 238 1 8 HELIX 11 11 LEU A 247 VAL A 258 1 12 HELIX 12 12 THR B 5 ILE B 10 5 6 HELIX 13 13 ASN B 11 GLY B 28 1 18 HELIX 14 14 ASP B 30 GLY B 40 1 11 HELIX 15 15 ASN B 62 PHE B 74 1 13 HELIX 16 16 PRO B 84 ASN B 95 1 12 HELIX 17 17 ASN B 121 ARG B 135 1 15 HELIX 18 18 VAL B 152 LYS B 163 1 12 HELIX 19 19 ASP B 173 GLY B 185 1 13 HELIX 20 20 PRO B 211 LEU B 215 5 5 HELIX 21 21 SER B 231 TYR B 238 1 8 HELIX 22 22 LEU B 247 LEU B 259 1 13 SHEET 1 A 5 ASP A 77 VAL A 80 0 SHEET 2 A 5 LYS A 47 VAL A 51 1 N ILE A 50 O PHE A 79 SHEET 3 A 5 ILE A 99 ALA A 103 1 O LEU A 101 N GLY A 49 SHEET 4 A 5 PHE A 108 ASN A 112 -1 O HIS A 111 N ILE A 100 SHEET 5 A 5 MET A 118 ASN A 120 -1 O ALA A 119 N ALA A 110 SHEET 1 B 6 ILE A 187 PRO A 188 0 SHEET 2 B 6 ARG A 166 TYR A 170 1 N VAL A 167 O ILE A 187 SHEET 3 B 6 ASP A 143 VAL A 147 1 N VAL A 146 O TYR A 168 SHEET 4 B 6 PHE A 197 GLU A 202 1 O PHE A 201 N LEU A 145 SHEET 5 B 6 LEU A 215 SER A 222 1 O VAL A 220 N SER A 198 SHEET 6 B 6 GLN A 241 ILE A 243 1 O ILE A 243 N LEU A 221 SHEET 1 C 5 ASP B 77 VAL B 80 0 SHEET 2 C 5 LYS B 47 VAL B 51 1 N ILE B 50 O PHE B 79 SHEET 3 C 5 ILE B 99 ALA B 103 1 O LEU B 101 N GLY B 49 SHEET 4 C 5 PHE B 108 ASN B 112 -1 O LEU B 109 N MET B 102 SHEET 5 C 5 MET B 118 ASN B 120 -1 O ALA B 119 N ALA B 110 SHEET 1 D 6 ILE B 187 PRO B 188 0 SHEET 2 D 6 ARG B 166 TYR B 170 1 N VAL B 167 O ILE B 187 SHEET 3 D 6 ASP B 143 VAL B 147 1 N VAL B 146 O TYR B 168 SHEET 4 D 6 ILE B 199 GLU B 202 1 O PHE B 201 N LEU B 145 SHEET 5 D 6 VAL B 220 SER B 222 1 O SER B 222 N ILE B 200 SHEET 6 D 6 GLN B 241 ILE B 243 1 O ILE B 243 N LEU B 221 SSBOND 1 CYS A 206 CYS B 206 1555 1555 2.05 LINK OE1 GLU A 202 NA NA A 902 1555 1555 2.29 LINK OE2 GLU A 202 NA NA A 902 1555 1555 3.12 LINK O THR A 204 NA NA A 902 1555 1555 2.26 LINK O CYS A 206 NA NA A 902 1555 1555 2.26 LINK O GLU A 245 MG MG A 903 1555 1555 2.89 LINK O7N NAI A 901 MG MG A 903 1555 1555 2.19 LINK NA NA A 902 O HOH A1001 1555 1555 2.95 LINK O THR B 204 NA NA B 303 1555 1555 2.27 LINK O CYS B 206 NA NA B 303 1555 1555 2.26 LINK O PRO B 227 NA NA B 303 1555 1555 2.27 LINK OE2 GLU B 245 MG MG B 304 1555 1555 2.86 LINK O7N NAI B 302 MG MG B 304 1555 1555 2.21 LINK NA NA B 303 O HOH B 407 1555 1555 3.01 CISPEP 1 ILE A 226 PRO A 227 0 4.79 CISPEP 2 ILE B 226 PRO B 227 0 0.67 SITE 1 AC1 25 ALA A 2 ASN A 121 THR A 125 GLY A 148 SITE 2 AC1 25 GLY A 150 LYS A 151 VAL A 152 ASP A 171 SITE 3 AC1 25 ALA A 172 LEU A 176 ALA A 203 THR A 204 SITE 4 AC1 25 PRO A 205 THR A 209 PRO A 224 ILE A 226 SITE 5 AC1 25 GLU A 245 PRO A 246 MG A 903 0TF A 904 SITE 6 AC1 25 HOH A1003 HOH A1005 HOH A1008 HOH A1025 SITE 7 AC1 25 ALA B 207 SITE 1 AC2 4 GLU A 202 THR A 204 CYS A 206 HOH A1001 SITE 1 AC3 6 TYR A 129 GLU A 245 LEU A 247 ILE A 249 SITE 2 AC3 6 GLY A 250 NAI A 901 SITE 1 AC4 16 LEU A 4 PRO A 52 VAL A 53 GLY A 58 SITE 2 AC4 16 ILE A 59 ILE A 60 PHE A 63 ALA A 103 SITE 3 AC4 16 ASN A 121 PRO A 246 LEU A 247 NAI A 901 SITE 4 AC4 16 HOH A1002 HOH A1010 HOH A1012 HOH A1018 SITE 1 AC5 17 LEU B 3 LEU B 4 VAL B 53 GLY B 58 SITE 2 AC5 17 ILE B 59 ILE B 60 PHE B 63 ALA B 103 SITE 3 AC5 17 ASP B 104 PRO B 246 LEU B 247 NAI B 302 SITE 4 AC5 17 HOH B 403 HOH B 404 HOH B 406 HOH B 441 SITE 5 AC5 17 HOH B 556 SITE 1 AC6 26 ALA A 207 ALA B 2 ASN B 121 THR B 125 SITE 2 AC6 26 GLY B 150 LYS B 151 VAL B 152 TYR B 170 SITE 3 AC6 26 ASP B 171 ALA B 172 LEU B 176 ALA B 203 SITE 4 AC6 26 THR B 204 PRO B 205 CYS B 206 THR B 209 SITE 5 AC6 26 PRO B 224 ILE B 226 GLU B 245 PRO B 246 SITE 6 AC6 26 0TF B 301 MG B 304 HOH B 401 HOH B 402 SITE 7 AC6 26 HOH B 415 HOH B 501 SITE 1 AC7 5 GLU B 202 THR B 204 CYS B 206 PRO B 227 SITE 2 AC7 5 HOH B 407 SITE 1 AC8 6 TYR B 129 GLU B 245 LEU B 247 ILE B 249 SITE 2 AC8 6 GLY B 250 NAI B 302 CRYST1 48.383 142.440 167.305 90.00 90.00 90.00 C 2 2 21 16 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 0.020668 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007020 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005977 0.00000 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 -0.506347 0.016010 0.862181 -0.67394 1 MTRIX2 2 -0.018087 -0.999805 0.007943 37.11193 1 MTRIX3 2 0.862140 -0.011572 0.506538 0.30283 1