HEADER OXIDOREDUCTASE 10-DEC-11 3V1U TITLE CRYSTAL STRUCTURE OF A BETA-KETOACYL REDUCTASE FABG4 FROM TITLE 2 MYCOBACTERIUM TUBERCULOSIS H37RV COMPLEXED WITH NAD+ AND HEXANOYL-COA TITLE 3 AT 2.5 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-OXOACYL-(ACYL-CARRIER-PROTEIN) REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROBABLE 3-OXOACYL-[ACYL-CARRIER PROTEIN] REDUCTASE FABG4 COMPND 5 (3-KETOACYL-ACYL CARRIER PROTEIN REDUCTASE); COMPND 6 EC: 1.1.1.100; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: FABG-1, FABG4, MT0256, RV0242C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: M15; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE30 KEYWDS ROSSMANN FOLD, KETOREDUCTASE, HIGH MOLECULAR WEIGHT FABG(HMWFABG), KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR D.DUTTA,S.BHATTACHARYYA,A.K.DAS REVDAT 4 08-NOV-23 3V1U 1 REMARK SEQADV REVDAT 3 12-MAR-14 3V1U 1 JRNL REVDAT 2 05-DEC-12 3V1U 1 JRNL REVDAT 1 28-NOV-12 3V1U 0 JRNL AUTH D.DUTTA,S.BHATTACHARYYA,A.ROYCHOWDHURY,R.BISWAS,A.K.DAS JRNL TITL CRYSTAL STRUCTURE OF HEXANOYL-COA BOUND TO BETA-KETOACYL JRNL TITL 2 REDUCTASE FABG4 OF MYCOBACTERIUM TUBERCULOSIS JRNL REF BIOCHEM.J. V. 450 127 2013 JRNL REFN ISSN 0264-6021 JRNL PMID 23163771 JRNL DOI 10.1042/BJ20121107 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0095 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 89.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 15469 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.190 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 : 825 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) : 1081 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.27 REMARK 3 BIN R VALUE (WORKING SET) : 0.2960 REMARK 3 BIN FREE R VALUE SET COUNT : 79 REMARK 3 BIN FREE R VALUE : 0.3660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2986 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 108 REMARK 3 SOLVENT ATOMS : 122 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.55000 REMARK 3 B22 (A**2) : 0.55000 REMARK 3 B33 (A**2) : -0.83000 REMARK 3 B12 (A**2) : 0.28000 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): 0.542 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.280 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.227 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.527 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3151 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4295 ; 1.790 ; 2.009 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 415 ; 6.535 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;36.536 ;23.739 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 462 ;18.501 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;20.543 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 507 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2354 ; 0.008 ; 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): 2051 ; 0.861 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3248 ; 1.588 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1100 ; 2.275 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1047 ; 3.776 ; 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 3V1U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-DEC-11. REMARK 100 THE DEPOSITION ID IS D_1000069488. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-DEC-11 REMARK 200 TEMPERATURE (KELVIN) : 103 REMARK 200 PH : 6.5 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 : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XSCALE REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.9, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16296 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.497 REMARK 200 RESOLUTION RANGE LOW (A) : 89.252 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10300 REMARK 200 FOR THE DATA SET : 18.9000 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) : 2.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.84800 REMARK 200 R SYM FOR SHELL (I) : 0.84800 REMARK 200 FOR SHELL : 0.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.1.4 REMARK 200 STARTING MODEL: PDB ENTRY 3Q6I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 45% POLYPROPYLENE GLYCOL, 0.1M MES PH REMARK 280 6.5, 10MM HEXANOYL COA, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.69800 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.34900 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.34900 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 50.69800 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 -50.69800 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 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 PRO A 3 REMARK 465 LYS A 4 REMARK 465 ARG A 5 REMARK 465 SER A 6 REMARK 465 SER A 7 REMARK 465 ASP A 8 REMARK 465 LEU A 9 REMARK 465 PHE A 10 REMARK 465 SER A 11 REMARK 465 GLN A 12 REMARK 465 VAL A 13 REMARK 465 VAL A 14 REMARK 465 ASN A 15 REMARK 465 SER A 16 REMARK 465 GLY A 17 REMARK 465 PRO A 18 REMARK 465 GLY A 19 REMARK 465 SER A 20 REMARK 465 PHE A 21 REMARK 465 LEU A 22 REMARK 465 ALA A 23 REMARK 465 ARG A 24 REMARK 465 GLN A 25 REMARK 465 LEU A 26 REMARK 465 GLY A 27 REMARK 465 VAL A 28 REMARK 465 ASN A 73 REMARK 465 ASN A 74 REMARK 465 LEU A 75 REMARK 465 GLY A 76 REMARK 465 GLY A 77 REMARK 465 ARG A 78 REMARK 465 TRP A 79 REMARK 465 THR A 398 REMARK 465 ALA A 399 REMARK 465 ALA A 400 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 LYS A 66 CG CD CE NZ REMARK 470 LYS A 100 CG CD CE NZ REMARK 470 ARG A 111 CG CD NE CZ NH1 NH2 REMARK 470 THR A 395 OG1 CG2 REMARK 470 MET A 397 CG SD CE REMARK 470 LEU A 403 CD1 CD2 REMARK 470 ARG A 406 CD NE CZ NH1 NH2 REMARK 470 GLU A 407 CG CD OE1 OE2 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 LEU A 345 CA - CB - CG ANGL. DEV. = -15.4 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 SER A 82 104.98 2.75 REMARK 500 ARG A 115 124.41 -34.06 REMARK 500 THR A 125 114.80 -35.01 REMARK 500 ALA A 187 -36.69 -34.28 REMARK 500 ALA A 249 96.05 20.85 REMARK 500 GLU A 250 -39.85 93.21 REMARK 500 ALA A 270 132.96 -38.71 REMARK 500 ASN A 306 48.98 -92.98 REMARK 500 LEU A 320 -58.28 -128.93 REMARK 500 SER A 346 -155.18 -89.61 REMARK 500 PRO A 402 129.96 -36.29 REMARK 500 LEU A 403 24.00 -75.85 REMARK 500 GLU A 407 -8.75 -56.95 REMARK 500 VAL A 408 -63.18 -103.86 REMARK 500 SER A 433 130.11 -36.61 REMARK 500 SER A 436 42.97 -97.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 114 ARG A 115 149.75 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 HXC A 502 REMARK 610 ZPG A 503 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HXC A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZPG A 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3LLS RELATED DB: PDB REMARK 900 RELATED ID: 3M1L RELATED DB: PDB REMARK 900 RELATED ID: 3Q6I RELATED DB: PDB REMARK 900 RELATED ID: 4FW8 RELATED DB: PDB DBREF 3V1U A 1 454 UNP O53665 O53665_MYCTU 1 454 SEQADV 3V1U HIS A -7 UNP O53665 EXPRESSION TAG SEQADV 3V1U HIS A -6 UNP O53665 EXPRESSION TAG SEQADV 3V1U HIS A -5 UNP O53665 EXPRESSION TAG SEQADV 3V1U HIS A -4 UNP O53665 EXPRESSION TAG SEQADV 3V1U HIS A -3 UNP O53665 EXPRESSION TAG SEQADV 3V1U HIS A -2 UNP O53665 EXPRESSION TAG SEQADV 3V1U GLY A -1 UNP O53665 EXPRESSION TAG SEQADV 3V1U SER A 0 UNP O53665 EXPRESSION TAG SEQRES 1 A 462 HIS HIS HIS HIS HIS HIS GLY SER MET ALA PRO LYS ARG SEQRES 2 A 462 SER SER ASP LEU PHE SER GLN VAL VAL ASN SER GLY PRO SEQRES 3 A 462 GLY SER PHE LEU ALA ARG GLN LEU GLY VAL PRO GLN PRO SEQRES 4 A 462 GLU THR LEU ARG ARG TYR ARG ALA GLY GLU PRO PRO LEU SEQRES 5 A 462 THR GLY SER LEU LEU ILE GLY GLY ALA GLY ARG VAL VAL SEQRES 6 A 462 GLU PRO LEU ARG ALA ALA LEU GLU LYS ASP TYR ASP LEU SEQRES 7 A 462 VAL GLY ASN ASN LEU GLY GLY ARG TRP ALA ASP SER PHE SEQRES 8 A 462 GLY GLY LEU VAL PHE ASP ALA THR GLY ILE THR GLU PRO SEQRES 9 A 462 ALA GLY LEU LYS GLY LEU HIS GLU PHE PHE THR PRO VAL SEQRES 10 A 462 LEU ARG ASN LEU GLY ARG CYS GLY ARG VAL VAL VAL VAL SEQRES 11 A 462 GLY GLY THR PRO GLU ALA ALA ALA SER THR ASN GLU ARG SEQRES 12 A 462 ILE ALA GLN ARG ALA LEU GLU GLY PHE THR ARG SER LEU SEQRES 13 A 462 GLY LYS GLU LEU ARG ARG GLY ALA THR THR ALA LEU VAL SEQRES 14 A 462 TYR LEU SER PRO ASP ALA LYS PRO ALA ALA THR GLY LEU SEQRES 15 A 462 GLU SER THR MET ARG PHE LEU LEU SER ALA LYS SER ALA SEQRES 16 A 462 TYR VAL ASP GLY GLN VAL PHE SER VAL GLY ALA ASP ASP SEQRES 17 A 462 SER THR PRO PRO ALA ASP TRP GLU LYS PRO LEU ASP GLY SEQRES 18 A 462 LYS VAL ALA ILE VAL THR GLY ALA ALA ARG GLY ILE GLY SEQRES 19 A 462 ALA THR ILE ALA GLU VAL PHE ALA ARG ASP GLY ALA HIS SEQRES 20 A 462 VAL VAL ALA ILE ASP VAL GLU SER ALA ALA GLU ASN LEU SEQRES 21 A 462 ALA GLU THR ALA SER LYS VAL GLY GLY THR ALA LEU TRP SEQRES 22 A 462 LEU ASP VAL THR ALA ASP ASP ALA VAL ASP LYS ILE SER SEQRES 23 A 462 GLU HIS LEU ARG ASP HIS HIS GLY GLY LYS ALA ASP ILE SEQRES 24 A 462 LEU VAL ASN ASN ALA GLY ILE THR ARG ASP LYS LEU LEU SEQRES 25 A 462 ALA ASN MET ASP ASP ALA ARG TRP ASP ALA VAL LEU ALA SEQRES 26 A 462 VAL ASN LEU LEU ALA PRO LEU ARG LEU THR GLU GLY LEU SEQRES 27 A 462 VAL GLY ASN GLY SER ILE GLY GLU GLY GLY ARG VAL ILE SEQRES 28 A 462 GLY LEU SER SER ILE ALA GLY ILE ALA GLY ASN ARG GLY SEQRES 29 A 462 GLN THR ASN TYR ALA THR THR LYS ALA GLY MET ILE GLY SEQRES 30 A 462 ILE THR GLN ALA LEU ALA PRO GLY LEU ALA ALA LYS GLY SEQRES 31 A 462 ILE THR ILE ASN ALA VAL ALA PRO GLY PHE ILE GLU THR SEQRES 32 A 462 GLN MET THR ALA ALA ILE PRO LEU ALA THR ARG GLU VAL SEQRES 33 A 462 GLY ARG ARG LEU ASN SER LEU LEU GLN GLY GLY GLN PRO SEQRES 34 A 462 VAL ASP VAL ALA GLU ALA ILE ALA TYR PHE ALA SER PRO SEQRES 35 A 462 ALA SER ASN ALA VAL THR GLY ASN VAL ILE ARG VAL CYS SEQRES 36 A 462 GLY GLN ALA MET ILE GLY ALA HET NAD A 501 44 HET HXC A 502 51 HET ZPG A 503 13 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM HXC HEXANOYL-COENZYME A HETNAM ZPG (2S,5R,8R,11S,14S,17S,21R)-5,8,11,14,17-PENTAMETHYL-4, HETNAM 2 ZPG 7,10,13,16,19-HEXAOXADOCOSANE-2,21-DIOL FORMUL 2 NAD C21 H27 N7 O14 P2 FORMUL 3 HXC C27 H46 N7 O17 P3 S FORMUL 4 ZPG C21 H44 O8 FORMUL 5 HOH *122(H2 O) HELIX 1 1 VAL A 56 GLU A 65 1 10 HELIX 2 2 GLU A 95 GLY A 98 5 4 HELIX 3 3 LEU A 99 LEU A 110 1 12 HELIX 4 4 PRO A 126 ALA A 129 5 4 HELIX 5 5 SER A 131 LYS A 150 1 20 HELIX 6 6 ALA A 171 GLY A 173 5 3 HELIX 7 7 LEU A 174 LEU A 182 1 9 HELIX 8 8 SER A 183 ALA A 187 5 5 HELIX 9 9 ARG A 223 ASP A 236 1 14 HELIX 10 10 VAL A 245 ALA A 249 5 5 HELIX 11 11 GLU A 250 GLY A 260 1 11 HELIX 12 12 ASP A 272 GLY A 286 1 15 HELIX 13 13 ASP A 308 LEU A 320 1 13 HELIX 14 14 LEU A 320 ASN A 333 1 14 HELIX 15 15 SER A 347 GLY A 353 1 7 HELIX 16 16 GLN A 357 LYS A 381 1 25 HELIX 17 17 THR A 405 ARG A 410 1 6 HELIX 18 18 GLN A 420 SER A 433 1 14 SHEET 1 A 5 SER A 47 GLY A 52 0 SHEET 2 A 5 PHE A 83 ASP A 89 1 O GLY A 84 N SER A 47 SHEET 3 A 5 LEU A 113 GLY A 124 1 O GLY A 114 N PHE A 83 SHEET 4 A 5 THR A 157 LEU A 163 1 O THR A 157 N VAL A 119 SHEET 5 A 5 GLN A 192 VAL A 196 1 O VAL A 196 N TYR A 162 SHEET 1 B 7 THR A 262 TRP A 265 0 SHEET 2 B 7 HIS A 239 ASP A 244 1 N ALA A 242 O LEU A 264 SHEET 3 B 7 VAL A 215 THR A 219 1 N VAL A 218 O VAL A 241 SHEET 4 B 7 ILE A 291 ASN A 294 1 O ILE A 291 N ILE A 217 SHEET 5 B 7 ARG A 341 LEU A 345 1 O ARG A 341 N LEU A 292 SHEET 6 B 7 THR A 384 PRO A 390 1 O ASN A 386 N GLY A 344 SHEET 7 B 7 VAL A 443 VAL A 446 1 O ILE A 444 N ALA A 389 CISPEP 1 VAL A 71 GLY A 72 0 6.64 CISPEP 2 THR A 395 GLN A 396 0 -8.24 SITE 1 AC1 25 GLY A 220 ARG A 223 GLY A 224 ILE A 225 SITE 2 AC1 25 ASP A 244 VAL A 245 LEU A 266 ASP A 267 SITE 3 AC1 25 VAL A 268 ASN A 295 ALA A 296 ILE A 298 SITE 4 AC1 25 VAL A 318 LEU A 345 SER A 346 SER A 347 SITE 5 AC1 25 TYR A 360 LYS A 364 PRO A 390 GLY A 391 SITE 6 AC1 25 ILE A 393 GLN A 396 HXC A 502 HOH A 630 SITE 7 AC1 25 HOH A 709 SITE 1 AC2 12 GLU A 151 ARG A 153 GLY A 297 THR A 299 SITE 2 AC2 12 ASP A 301 LYS A 302 LEU A 303 ASN A 306 SITE 3 AC2 12 ASN A 354 ARG A 355 NAD A 501 HOH A 669 SITE 1 AC3 3 GLU A 338 ALA A 379 ALA A 380 CRYST1 103.059 103.059 76.047 90.00 90.00 120.00 P 32 2 1 6 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 0.009703 0.005602 0.000000 0.00000 SCALE2 0.000000 0.011204 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013150 0.00000