PDB Short entry for 3NYQ HEADER LIGASE 15-JUL-10 3NYQ TITLE MALONYL-COA LIGASE TERNARY PRODUCT COMPLEX WITH METHYLMALONYL-COA AND TITLE 2 AMP BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: MALONYL-COA LIGASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES COELICOLOR; SOURCE 3 ORGANISM_TAXID: 1902; SOURCE 4 GENE: MATB, SCC24.15, SCO2444; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS A/B TOPOLOGY ABABA SANDWICH BETA-BARREL ADENYLATE-FORMING ENZYME KEYWDS 2 FOLD, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR A.J.HUGHES,A.T.KEATINGE-CLAY REVDAT 2 21-FEB-24 3NYQ 1 REMARK SEQADV LINK REVDAT 1 30-MAR-11 3NYQ 0 JRNL AUTH A.J.HUGHES,A.KEATINGE-CLAY JRNL TITL ENZYMATIC EXTENDER UNIT GENERATION FOR IN VITRO POLYKETIDE JRNL TITL 2 SYNTHASE REACTIONS: STRUCTURAL AND FUNCTIONAL SHOWCASING OF JRNL TITL 3 STREPTOMYCES COELICOLOR MATB. JRNL REF CHEM.BIOL. V. 18 165 2011 JRNL REFN ISSN 1074-5521 JRNL PMID 21338915 JRNL DOI 10.1016/J.CHEMBIOL.2010.12.014 REMARK 2 REMARK 2 RESOLUTION. 1.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 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) : 1.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 76.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 83693 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4436 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) : 1.43 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.47 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5091 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.39 REMARK 3 BIN R VALUE (WORKING SET) : 0.2610 REMARK 3 BIN FREE R VALUE SET COUNT : 263 REMARK 3 BIN FREE R VALUE : 0.2830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3378 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 404 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.39000 REMARK 3 B22 (A**2) : 0.05000 REMARK 3 B33 (A**2) : -0.44000 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): 0.068 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.068 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.039 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.962 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3505 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4796 ; 1.770 ; 2.005 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 457 ; 6.863 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 134 ;33.626 ;22.164 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 502 ;13.490 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 37 ;20.218 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 554 ; 0.200 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2691 ; 0.018 ; 0.022 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): 2291 ; 1.589 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3660 ; 2.550 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1214 ; 3.759 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1136 ; 5.327 ; 4.500 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3NYQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUL-10. REMARK 100 THE DEPOSITION ID IS D_1000060446. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JAN-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL, SI(111) LIQUID REMARK 200 N2 COOLED REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 91903 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.430 REMARK 200 RESOLUTION RANGE LOW (A) : 76.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.29200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHASER MR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 33% PEG 4000, 0.1M MAGNESIUM CHLORIDE, REMARK 280 PH 9.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 76.69550 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 76.69550 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 36.68800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.39300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 36.68800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.39300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 76.69550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 36.68800 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 43.39300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 76.69550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 36.68800 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 43.39300 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -101.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 153.39100 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 -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 SER A 3 REMARK 465 GLY A 47 REMARK 465 ALA A 48 REMARK 465 GLY A 49 REMARK 465 GLU A 319 REMARK 465 GLU A 320 REMARK 465 ASP A 321 REMARK 465 GLY A 322 REMARK 465 THR A 323 REMARK 465 ASN A 472 REMARK 465 ASP A 473 REMARK 465 MET A 474 REMARK 465 GLY A 475 REMARK 465 LYS A 476 REMARK 465 ILE A 477 REMARK 465 MET A 478 REMARK 465 LYS A 479 REMARK 465 ARG A 480 REMARK 465 ALA A 481 REMARK 465 LEU A 482 REMARK 465 ASN A 483 REMARK 465 ARG A 484 REMARK 465 ASP A 485 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 HOH A 672 O HOH A 890 1.94 REMARK 500 CD ARG A 158 O HOH A 890 1.98 REMARK 500 O HOH A 736 O HOH A 896 1.99 REMARK 500 O HOH A 671 O HOH A 890 2.15 REMARK 500 O HOH A 901 O HOH A 902 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 NH1 ARG A 124 O HOH A 567 3555 2.15 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 SER A 261 -18.82 89.06 REMARK 500 LEU A 290 -143.28 45.08 REMARK 500 GLU A 331 -38.25 -138.56 REMARK 500 ALA A 385 -24.51 -141.52 REMARK 500 LEU A 454 -84.39 -107.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 MCA A 486 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 499 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 838 O REMARK 620 2 HOH A 839 O 89.9 REMARK 620 3 HOH A 840 O 86.6 96.1 REMARK 620 4 HOH A 841 O 92.6 88.9 175.0 REMARK 620 5 HOH A 842 O 175.6 89.2 89.1 91.8 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MCA A 486 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP A 487 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 497 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 498 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 499 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ITE RELATED DB: PDB REMARK 900 RELATED ID: 3E7W RELATED DB: PDB REMARK 900 RELATED ID: 1T5D RELATED DB: PDB REMARK 900 RELATED ID: 2D1R RELATED DB: PDB REMARK 900 RELATED ID: 1RY2 RELATED DB: PDB REMARK 900 RELATED ID: 1PG3 RELATED DB: PDB DBREF 3NYQ A 1 485 UNP Q9L0A2 Q9L0A2_STRCO 1 485 SEQADV 3NYQ MET A -19 UNP Q9L0A2 EXPRESSION TAG SEQADV 3NYQ GLY A -18 UNP Q9L0A2 EXPRESSION TAG SEQADV 3NYQ SER A -17 UNP Q9L0A2 EXPRESSION TAG SEQADV 3NYQ SER A -16 UNP Q9L0A2 EXPRESSION TAG SEQADV 3NYQ HIS A -15 UNP Q9L0A2 EXPRESSION TAG SEQADV 3NYQ HIS A -14 UNP Q9L0A2 EXPRESSION TAG SEQADV 3NYQ HIS A -13 UNP Q9L0A2 EXPRESSION TAG SEQADV 3NYQ HIS A -12 UNP Q9L0A2 EXPRESSION TAG SEQADV 3NYQ HIS A -11 UNP Q9L0A2 EXPRESSION TAG SEQADV 3NYQ HIS A -10 UNP Q9L0A2 EXPRESSION TAG SEQADV 3NYQ SER A -9 UNP Q9L0A2 EXPRESSION TAG SEQADV 3NYQ SER A -8 UNP Q9L0A2 EXPRESSION TAG SEQADV 3NYQ GLY A -7 UNP Q9L0A2 EXPRESSION TAG SEQADV 3NYQ LEU A -6 UNP Q9L0A2 EXPRESSION TAG SEQADV 3NYQ VAL A -5 UNP Q9L0A2 EXPRESSION TAG SEQADV 3NYQ PRO A -4 UNP Q9L0A2 EXPRESSION TAG SEQADV 3NYQ ARG A -3 UNP Q9L0A2 EXPRESSION TAG SEQADV 3NYQ GLY A -2 UNP Q9L0A2 EXPRESSION TAG SEQADV 3NYQ SER A -1 UNP Q9L0A2 EXPRESSION TAG SEQADV 3NYQ HIS A 0 UNP Q9L0A2 EXPRESSION TAG SEQRES 1 A 505 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 505 LEU VAL PRO ARG GLY SER HIS MET SER SER LEU PHE PRO SEQRES 3 A 505 ALA LEU SER PRO ALA PRO THR GLY ALA PRO ALA ASP ARG SEQRES 4 A 505 PRO ALA LEU ARG PHE GLY GLU ARG SER LEU THR TYR ALA SEQRES 5 A 505 GLU LEU ALA ALA ALA ALA GLY ALA THR ALA GLY ARG ILE SEQRES 6 A 505 GLY GLY ALA GLY ARG VAL ALA VAL TRP ALA THR PRO ALA SEQRES 7 A 505 MET GLU THR GLY VAL ALA VAL VAL ALA ALA LEU LEU ALA SEQRES 8 A 505 GLY VAL ALA ALA VAL PRO LEU ASN PRO LYS SER GLY ASP SEQRES 9 A 505 LYS GLU LEU ALA HIS ILE LEU SER ASP SER ALA PRO SER SEQRES 10 A 505 LEU VAL LEU ALA PRO PRO ASP ALA GLU LEU PRO PRO ALA SEQRES 11 A 505 LEU GLY ALA LEU GLU ARG VAL ASP VAL ASP VAL ARG ALA SEQRES 12 A 505 ARG GLY ALA VAL PRO GLU ASP GLY ALA ASP ASP GLY ASP SEQRES 13 A 505 PRO ALA LEU VAL VAL TYR THR SER GLY THR THR GLY PRO SEQRES 14 A 505 PRO LYS GLY ALA VAL ILE PRO ARG ARG ALA LEU ALA THR SEQRES 15 A 505 THR LEU ASP ALA LEU ALA ASP ALA TRP GLN TRP THR GLY SEQRES 16 A 505 GLU ASP VAL LEU VAL GLN GLY LEU PRO LEU PHE HIS VAL SEQRES 17 A 505 HIS GLY LEU VAL LEU GLY ILE LEU GLY PRO LEU ARG ARG SEQRES 18 A 505 GLY GLY SER VAL ARG HIS LEU GLY ARG PHE SER THR GLU SEQRES 19 A 505 GLY ALA ALA ARG GLU LEU ASN ASP GLY ALA THR MET LEU SEQRES 20 A 505 PHE GLY VAL PRO THR MET TYR HIS ARG ILE ALA GLU THR SEQRES 21 A 505 LEU PRO ALA ASP PRO GLU LEU ALA LYS ALA LEU ALA GLY SEQRES 22 A 505 ALA ARG LEU LEU VAL SER GLY SER ALA ALA LEU PRO VAL SEQRES 23 A 505 HIS ASP HIS GLU ARG ILE ALA ALA ALA THR GLY ARG ARG SEQRES 24 A 505 VAL ILE GLU ARG TYR GLY MET THR GLU THR LEU MET ASN SEQRES 25 A 505 THR SER VAL ARG ALA ASP GLY GLU PRO ARG ALA GLY THR SEQRES 26 A 505 VAL GLY VAL PRO LEU PRO GLY VAL GLU LEU ARG LEU VAL SEQRES 27 A 505 GLU GLU ASP GLY THR PRO ILE ALA ALA LEU ASP GLY GLU SEQRES 28 A 505 SER VAL GLY GLU ILE GLN VAL ARG GLY PRO ASN LEU PHE SEQRES 29 A 505 THR GLU TYR LEU ASN ARG PRO ASP ALA THR ALA ALA ALA SEQRES 30 A 505 PHE THR GLU ASP GLY PHE PHE ARG THR GLY ASP MET ALA SEQRES 31 A 505 VAL ARG ASP PRO ASP GLY TYR VAL ARG ILE VAL GLY ARG SEQRES 32 A 505 LYS ALA THR ASP LEU ILE LYS SER GLY GLY TYR LYS ILE SEQRES 33 A 505 GLY ALA GLY GLU ILE GLU ASN ALA LEU LEU GLU HIS PRO SEQRES 34 A 505 GLU VAL ARG GLU ALA ALA VAL THR GLY GLU PRO ASP PRO SEQRES 35 A 505 ASP LEU GLY GLU ARG ILE VAL ALA TRP ILE VAL PRO ALA SEQRES 36 A 505 ASP PRO ALA ALA PRO PRO ALA LEU GLY THR LEU ALA ASP SEQRES 37 A 505 HIS VAL ALA ALA ARG LEU ALA PRO HIS LYS ARG PRO ARG SEQRES 38 A 505 VAL VAL ARG TYR LEU ASP ALA VAL PRO ARG ASN ASP MET SEQRES 39 A 505 GLY LYS ILE MET LYS ARG ALA LEU ASN ARG ASP HET MCA A 486 29 HET AMP A 487 23 HET CL A 497 1 HET CL A 498 1 HET MG A 499 1 HETNAM MCA METHYLMALONYL-COENZYME A HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM CL CHLORIDE ION HETNAM MG MAGNESIUM ION FORMUL 2 MCA C25 H40 N7 O19 P3 S FORMUL 3 AMP C10 H14 N5 O7 P FORMUL 4 CL 2(CL 1-) FORMUL 6 MG MG 2+ FORMUL 7 HOH *404(H2 O) HELIX 1 1 GLY A 14 ASP A 18 5 5 HELIX 2 2 TYR A 31 GLY A 43 1 13 HELIX 3 3 ALA A 58 GLY A 72 1 15 HELIX 4 4 GLY A 83 ALA A 95 1 13 HELIX 5 5 PRO A 108 GLY A 112 5 5 HELIX 6 6 ARG A 157 GLN A 172 1 16 HELIX 7 7 HIS A 187 VAL A 192 1 6 HELIX 8 8 ILE A 195 GLY A 202 1 8 HELIX 9 9 SER A 212 ASN A 221 1 10 HELIX 10 10 VAL A 230 LEU A 241 1 12 HELIX 11 11 ASP A 244 ALA A 254 1 11 HELIX 12 12 PRO A 265 GLY A 277 1 13 HELIX 13 13 ARG A 350 ALA A 357 1 8 HELIX 14 14 GLY A 397 LEU A 406 1 10 HELIX 15 15 ALA A 442 LEU A 454 1 13 HELIX 16 16 ALA A 455 ARG A 459 5 5 SHEET 1 A 9 ARG A 27 THR A 30 0 SHEET 2 A 9 PRO A 20 PHE A 24 -1 N PHE A 24 O ARG A 27 SHEET 3 A 9 SER A 204 HIS A 207 1 O HIS A 207 N ARG A 23 SHEET 4 A 9 VAL A 178 GLN A 181 1 N LEU A 179 O ARG A 206 SHEET 5 A 9 MET A 226 GLY A 229 1 O MET A 226 N VAL A 180 SHEET 6 A 9 LEU A 256 SER A 259 1 O VAL A 258 N LEU A 227 SHEET 7 A 9 ILE A 281 MET A 286 1 O ILE A 281 N LEU A 257 SHEET 8 A 9 LEU A 290 SER A 294 -1 O ASN A 292 N TYR A 284 SHEET 9 A 9 VAL A 308 PRO A 309 -1 O VAL A 308 N SER A 294 SHEET 1 B 4 ALA A 75 LEU A 78 0 SHEET 2 B 4 VAL A 51 TRP A 54 1 N VAL A 53 O LEU A 78 SHEET 3 B 4 LEU A 98 ALA A 101 1 O LEU A 100 N ALA A 52 SHEET 4 B 4 GLU A 115 ASP A 118 1 O VAL A 117 N VAL A 99 SHEET 1 C 3 PRO A 137 THR A 143 0 SHEET 2 C 3 LYS A 151 PRO A 156 -1 O ILE A 155 N ALA A 138 SHEET 3 C 3 GLU A 346 TYR A 347 -1 O GLU A 346 N VAL A 154 SHEET 1 D 4 GLU A 314 VAL A 318 0 SHEET 2 D 4 GLY A 334 ARG A 339 -1 O ARG A 339 N GLU A 314 SHEET 3 D 4 PHE A 364 ARG A 372 -1 O PHE A 364 N VAL A 338 SHEET 4 D 4 VAL A 378 ARG A 383 -1 O ARG A 379 N VAL A 371 SHEET 1 E 2 ILE A 389 SER A 391 0 SHEET 2 E 2 TYR A 394 ILE A 396 -1 O ILE A 396 N ILE A 389 SHEET 1 F 3 VAL A 411 ASP A 421 0 SHEET 2 F 3 GLY A 425 PRO A 434 -1 O TRP A 431 N ALA A 415 SHEET 3 F 3 VAL A 462 TYR A 465 1 O ARG A 464 N ILE A 432 LINK MG MG A 499 O HOH A 838 1555 1555 2.02 LINK MG MG A 499 O HOH A 839 1555 1555 2.02 LINK MG MG A 499 O HOH A 840 1555 1555 2.10 LINK MG MG A 499 O HOH A 841 1555 1555 2.09 LINK MG MG A 499 O HOH A 842 1555 1555 2.09 CISPEP 1 SER A 9 PRO A 10 0 -1.45 SITE 1 AC1 21 PRO A 184 HIS A 189 THR A 232 ARG A 236 SITE 2 AC1 21 SER A 261 ARG A 283 GLY A 285 MET A 286 SITE 3 AC1 21 THR A 287 MET A 291 LYS A 390 GLY A 392 SITE 4 AC1 21 GLY A 393 TYR A 394 ARG A 461 AMP A 487 SITE 5 AC1 21 HOH A 500 HOH A 572 HOH A 687 HOH A 853 SITE 6 AC1 21 HOH A 859 SITE 1 AC2 16 SER A 261 ALA A 262 ALA A 263 ARG A 283 SITE 2 AC2 16 GLY A 285 MET A 286 THR A 287 VAL A 306 SITE 3 AC2 16 ASP A 368 LYS A 390 LYS A 395 MCA A 486 SITE 4 AC2 16 HOH A 540 HOH A 659 HOH A 783 HOH A 891 SITE 1 AC3 5 PHE A 24 ARG A 27 ALA A 58 MET A 59 SITE 2 AC3 5 HOH A 824 SITE 1 AC4 4 ASN A 79 PRO A 456 HIS A 457 HOH A 622 SITE 1 AC5 6 GLU A 331 HOH A 838 HOH A 839 HOH A 840 SITE 2 AC5 6 HOH A 841 HOH A 842 CRYST1 73.376 86.786 153.391 90.00 90.00 90.00 C 2 2 21 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 0.013628 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011523 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006519 0.00000