HEADER OXIDOREDUCTASE 09-MAR-13 4JK3 TITLE PYLD HOLOENZYME (SEMET) 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: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS PYRROLYSINE, 22ND AMINO ACID, BIOSYNTHESIS, ROSSMANN FOLD, KEYWDS 2 DEHYDROGENASE, NAD, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR F.QUITTERER,P.BECK,A.BACHER,M.GROLL REVDAT 2 10-JUL-13 4JK3 1 JRNL REVDAT 1 12-JUN-13 4JK3 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. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 16865 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) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 887 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1179 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2580 REMARK 3 BIN FREE R VALUE SET COUNT : 62 REMARK 3 BIN FREE R VALUE : 0.2730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3798 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 92 REMARK 3 SOLVENT ATOMS : 49 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.91000 REMARK 3 B22 (A**2) : -5.59000 REMARK 3 B33 (A**2) : 2.69000 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): 1.033 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.315 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.226 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 21.626 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.938 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3964 ; 0.007 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5402 ; 1.361 ; 2.014 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 498 ; 5.374 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 158 ;35.585 ;25.696 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 608 ;17.317 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;13.565 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 630 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2950 ; 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): 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 : 2 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 5 A 259 REMARK 3 RESIDUE RANGE : A 901 A 903 REMARK 3 ORIGIN FOR THE GROUP (A): 80.2612 27.5105 -20.4510 REMARK 3 T TENSOR REMARK 3 T11: 0.0188 T22: 0.1993 REMARK 3 T33: 0.0246 T12: -0.0001 REMARK 3 T13: -0.0069 T23: -0.0180 REMARK 3 L TENSOR REMARK 3 L11: 0.9941 L22: 1.8065 REMARK 3 L33: 0.5123 L12: 1.1931 REMARK 3 L13: -0.2180 L23: -0.2295 REMARK 3 S TENSOR REMARK 3 S11: 0.0476 S12: 0.0220 S13: -0.0735 REMARK 3 S21: 0.1022 S22: -0.0182 S23: -0.0457 REMARK 3 S31: -0.0207 S32: 0.0018 S33: -0.0294 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 5 B 259 REMARK 3 RESIDUE RANGE : B 901 B 903 REMARK 3 ORIGIN FOR THE GROUP (A): 105.3078 8.5089 -33.3776 REMARK 3 T TENSOR REMARK 3 T11: 0.1477 T22: 0.1734 REMARK 3 T33: 0.0511 T12: -0.0681 REMARK 3 T13: 0.0626 T23: -0.0532 REMARK 3 L TENSOR REMARK 3 L11: 1.8726 L22: 5.1984 REMARK 3 L33: 0.1760 L12: 2.7797 REMARK 3 L13: 0.1649 L23: -0.1445 REMARK 3 S TENSOR REMARK 3 S11: -0.3569 S12: -0.0113 S13: -0.2415 REMARK 3 S21: -0.6142 S22: 0.3185 S23: -0.4964 REMARK 3 S31: -0.0223 S32: -0.1346 S33: 0.0384 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 4JK3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAR-13. REMARK 100 THE RCSB ID CODE IS RCSB078145. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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) : 0.9798 REMARK 200 MONOCHROMATOR : LN2 COOLED FIXED-EXIT. SI(111) REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.69300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS; 27% PEG3350; 0.2 M NACL, REMARK 280 PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+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 39.82500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 77.70000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.82500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 77.70000 REMARK 290 SMTRY3 4 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: 10690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 41660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -122.0 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 159.30000 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 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 MSE A 1 REMARK 465 ALA A 2 REMARK 465 LEU A 3 REMARK 465 LEU A 4 REMARK 465 GLY A 56 REMARK 465 ASN A 57 REMARK 465 GLY A 58 REMARK 465 ILE A 59 REMARK 465 MSE B 1 REMARK 465 ALA B 2 REMARK 465 LEU B 3 REMARK 465 LEU B 4 REMARK 465 GLY B 56 REMARK 465 ASN B 57 REMARK 465 GLY B 58 REMARK 465 ILE B 59 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 IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O THR B 27 O HOH B 1016 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 ASP A 85 -136.35 55.98 REMARK 500 ASP A 104 -164.36 -110.43 REMARK 500 PRO A 205 38.82 -87.25 REMARK 500 LEU A 247 -39.74 -158.42 REMARK 500 ASP B 85 -137.22 49.64 REMARK 500 ASP B 104 -163.88 -115.41 REMARK 500 PRO B 205 37.48 -85.74 REMARK 500 LEU B 247 -37.44 -158.02 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 B1017 DISTANCE = 5.17 ANGSTROMS 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 HOH A1019 O REMARK 620 2 THR A 204 O 131.4 REMARK 620 3 PRO A 227 O 68.6 114.6 REMARK 620 4 CYS A 206 O 120.1 106.7 75.7 REMARK 620 5 GLU A 202 OE2 77.9 84.6 146.2 127.2 REMARK 620 6 GLU A 202 OE1 103.8 92.8 149.6 84.2 43.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 902 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 206 O REMARK 620 2 HOH B1019 O 127.2 REMARK 620 3 THR B 204 O 104.3 124.1 REMARK 620 4 PRO B 227 O 74.1 72.9 106.9 REMARK 620 5 GLU B 202 OE1 90.9 103.3 95.1 155.7 REMARK 620 6 GLU B 202 OE2 135.7 72.5 86.1 144.4 44.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 903 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 NAD B 901 O7N REMARK 620 2 GLU B 245 OE2 121.1 REMARK 620 N 1 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 NAD A 901 O7N REMARK 620 2 GLU A 245 OE2 124.3 REMARK 620 3 TYR A 129 OH 115.3 90.5 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 NAD 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 NAD B 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 903 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4J43 RELATED DB: PDB REMARK 900 PYLD HOLOENZYME (NATIVE DATASET, 2.2 A RESOLUTION) REMARK 900 RELATED ID: 4J49 RELATED DB: PDB REMARK 900 RELATED ID: 4J4B RELATED DB: PDB REMARK 900 RELATED ID: 4J4H RELATED DB: PDB DBREF 4JK3 A 1 259 UNP Q46E80 Q46E80_METBF 5 263 DBREF 4JK3 B 1 259 UNP Q46E80 Q46E80_METBF 5 263 SEQRES 1 A 259 MSE ALA LEU LEU THR PRO ASP ASP LEU ILE ASN ILE ASN SEQRES 2 A 259 MSE 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 MSE PRO ASP VAL SER GLY TYR TYR GLU SEQRES 8 A 259 ALA VAL GLN ASN GLY ALA GLU ILE ILE LEU MSE ALA ASP SEQRES 9 A 259 ASP ARG THR PHE LEU ALA HIS ASN LEU LYS ASN GLY LYS SEQRES 10 A 259 MSE 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 MSE LEU TYR SER VAL LEU SEQRES 1 B 259 MSE ALA LEU LEU THR PRO ASP ASP LEU ILE ASN ILE ASN SEQRES 2 B 259 MSE 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 MSE PRO ASP VAL SER GLY TYR TYR GLU SEQRES 8 B 259 ALA VAL GLN ASN GLY ALA GLU ILE ILE LEU MSE ALA ASP SEQRES 9 B 259 ASP ARG THR PHE LEU ALA HIS ASN LEU LYS ASN GLY LYS SEQRES 10 B 259 MSE 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 MSE LEU TYR SER VAL LEU MODRES 4JK3 MSE A 14 MET SELENOMETHIONINE MODRES 4JK3 MSE A 83 MET SELENOMETHIONINE MODRES 4JK3 MSE A 102 MET SELENOMETHIONINE MODRES 4JK3 MSE A 118 MET SELENOMETHIONINE MODRES 4JK3 MSE A 254 MET SELENOMETHIONINE MODRES 4JK3 MSE B 14 MET SELENOMETHIONINE MODRES 4JK3 MSE B 83 MET SELENOMETHIONINE MODRES 4JK3 MSE B 102 MET SELENOMETHIONINE MODRES 4JK3 MSE B 118 MET SELENOMETHIONINE MODRES 4JK3 MSE B 254 MET SELENOMETHIONINE HET MSE A 14 8 HET MSE A 83 8 HET MSE A 102 8 HET MSE A 118 8 HET MSE A 254 8 HET MSE B 14 8 HET MSE B 83 8 HET MSE B 102 8 HET MSE B 118 8 HET MSE B 254 8 HET NAD A 901 44 HET NA A 902 1 HET MG A 903 1 HET NAD B 901 44 HET NA B 902 1 HET MG B 903 1 HETNAM MSE SELENOMETHIONINE HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM NA SODIUM ION HETNAM MG MAGNESIUM ION FORMUL 1 MSE 10(C5 H11 N O2 SE) FORMUL 3 NAD 2(C21 H27 N7 O14 P2) FORMUL 4 NA 2(NA 1+) FORMUL 5 MG 2(MG 2+) FORMUL 9 HOH *49(H2 O) HELIX 1 1 THR A 5 GLY A 28 1 24 HELIX 2 2 ASP A 30 GLY A 40 1 11 HELIX 3 3 GLY A 61 PHE A 74 1 14 HELIX 4 4 PRO A 84 ASN A 95 1 12 HELIX 5 5 ASN A 121 ARG A 135 1 15 HELIX 6 6 VAL A 152 LYS A 163 1 12 HELIX 7 7 ASP A 173 GLY A 185 1 13 HELIX 8 8 PRO A 211 ALA A 213 5 3 HELIX 9 9 SER A 231 TYR A 238 1 8 HELIX 10 10 LEU A 247 LEU A 259 1 13 HELIX 11 11 PRO B 6 GLY B 28 1 23 HELIX 12 12 ASP B 30 GLY B 40 1 11 HELIX 13 13 GLY B 61 PHE B 74 1 14 HELIX 14 14 PRO B 84 ASN B 95 1 12 HELIX 15 15 ASN B 121 ARG B 135 1 15 HELIX 16 16 VAL B 152 LYS B 163 1 12 HELIX 17 17 ASP B 173 GLY B 185 1 13 HELIX 18 18 PRO B 211 ALA B 213 5 3 HELIX 19 19 SER B 231 GLU B 239 1 9 HELIX 20 20 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 ILE A 50 1 N ILE A 50 O PHE A 79 SHEET 3 A 5 ILE A 99 ALA A 103 1 O ILE A 99 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 MSE 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 144 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 SER A 222 N ILE A 200 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 ILE B 50 1 N ILE B 50 O PHE B 79 SHEET 3 C 5 ILE B 99 ALA B 103 1 O ILE B 99 N GLY B 49 SHEET 4 C 5 PHE B 108 ASN B 112 -1 O HIS B 111 N ILE B 100 SHEET 5 C 5 MSE 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 144 O TYR B 168 SHEET 4 D 6 PHE B 197 GLU B 202 1 O PHE B 201 N LEU B 145 SHEET 5 D 6 LEU B 215 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 LINK C ASN A 13 N MSE A 14 1555 1555 1.33 LINK C MSE A 14 N GLN A 15 1555 1555 1.33 LINK C ASP A 82 N MSE A 83 1555 1555 1.33 LINK C MSE A 83 N PRO A 84 1555 1555 1.35 LINK C LEU A 101 N MSE A 102 1555 1555 1.33 LINK C MSE A 102 N ALA A 103 1555 1555 1.33 LINK C LYS A 117 N MSE A 118 1555 1555 1.33 LINK C MSE A 118 N ALA A 119 1555 1555 1.32 LINK C SER A 253 N MSE A 254 1555 1555 1.33 LINK C MSE A 254 N LEU A 255 1555 1555 1.34 LINK C ASN B 13 N MSE B 14 1555 1555 1.33 LINK C MSE B 14 N GLN B 15 1555 1555 1.33 LINK C ASP B 82 N MSE B 83 1555 1555 1.33 LINK C MSE B 83 N PRO B 84 1555 1555 1.35 LINK C LEU B 101 N MSE B 102 1555 1555 1.33 LINK C MSE B 102 N ALA B 103 1555 1555 1.33 LINK C LYS B 117 N MSE B 118 1555 1555 1.33 LINK C MSE B 118 N ALA B 119 1555 1555 1.33 LINK C SER B 253 N MSE B 254 1555 1555 1.34 LINK C MSE B 254 N LEU B 255 1555 1555 1.34 LINK NA NA A 902 O HOH A1019 1555 1555 2.54 LINK O CYS B 206 NA NA B 902 1555 1555 2.56 LINK O THR A 204 NA NA A 902 1555 1555 2.58 LINK NA NA B 902 O HOH B1019 1555 1555 2.58 LINK O THR B 204 NA NA B 902 1555 1555 2.61 LINK O PRO A 227 NA NA A 902 1555 1555 2.65 LINK O7N NAD B 901 MG MG B 903 1555 1555 2.66 LINK O CYS A 206 NA NA A 902 1555 1555 2.67 LINK O7N NAD A 901 MG MG A 903 1555 1555 2.70 LINK OE2 GLU A 245 MG MG A 903 1555 1555 2.71 LINK O PRO B 227 NA NA B 902 1555 1555 2.76 LINK OE1 GLU B 202 NA NA B 902 1555 1555 2.83 LINK OE2 GLU B 245 MG MG B 903 1555 1555 2.85 LINK OH TYR A 129 MG MG A 903 1555 1555 2.89 LINK OE2 GLU B 202 NA NA B 902 1555 1555 2.90 LINK OE2 GLU A 202 NA NA A 902 1555 1555 2.97 LINK OE1 GLU A 202 NA NA A 902 1555 1555 2.98 CISPEP 1 ILE A 226 PRO A 227 0 -0.06 CISPEP 2 ILE B 226 PRO B 227 0 0.71 SITE 1 AC1 23 ASN A 121 THR A 125 VAL A 147 GLY A 150 SITE 2 AC1 23 LYS A 151 VAL A 152 ASP A 171 ALA A 172 SITE 3 AC1 23 LEU A 176 ALA A 203 THR A 204 PRO A 205 SITE 4 AC1 23 CYS A 206 THR A 209 PRO A 224 ILE A 226 SITE 5 AC1 23 GLU A 245 PRO A 246 LEU A 247 MG A 903 SITE 6 AC1 23 HOH A1002 HOH A1011 HOH A1025 SITE 1 AC2 6 GLU A 202 THR A 204 CYS A 206 GLY A 225 SITE 2 AC2 6 PRO A 227 HOH A1019 SITE 1 AC3 6 TYR A 129 GLU A 245 LEU A 247 ILE A 249 SITE 2 AC3 6 GLY A 250 NAD A 901 SITE 1 AC4 21 ASN B 121 THR B 125 VAL B 147 GLY B 150 SITE 2 AC4 21 LYS B 151 VAL B 152 TYR B 170 ASP B 171 SITE 3 AC4 21 ALA B 172 LEU B 176 ALA B 203 THR B 204 SITE 4 AC4 21 PRO B 205 CYS B 206 PRO B 224 ILE B 226 SITE 5 AC4 21 GLU B 245 PRO B 246 LEU B 247 MG B 903 SITE 6 AC4 21 HOH B1001 SITE 1 AC5 5 GLU B 202 THR B 204 CYS B 206 PRO B 227 SITE 2 AC5 5 HOH B1019 SITE 1 AC6 6 TYR B 129 GLU B 245 LEU B 247 ILE B 249 SITE 2 AC6 6 GLY B 250 NAD B 901 CRYST1 79.650 155.400 39.570 90.00 90.00 90.00 P 21 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 0.012555 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006435 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025272 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 -0.306636 0.951004 -0.039582 103.15859 1 MTRIX2 2 0.950911 0.307899 0.031084 -74.22720 1 MTRIX3 2 0.041749 -0.028108 -0.998733 -57.93433 1