HEADER OXIDOREDUCTASE 07-OCT-10 3P4T TITLE CRYSTAL STRUCTURE OF A PUTATIVE ACYL-COA DEHYDROGENASE FROM TITLE 2 MYCOBACTERIUM SMEGMATIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE ACYL-COA DEHYDROGENASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 1.1.1.35; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM SMEGMATIS; SOURCE 3 ORGANISM_TAXID: 246196; SOURCE 4 STRAIN: ATCC 700084 / MC(2)155; SOURCE 5 GENE: MSMEG_5491; 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: AVA0421 KEYWDS SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR KEYWDS 2 INFECTIOUS DISEASE, OXIDOREDUCTASE, ACYL-COA DEHYDROGENASE, KEYWDS 3 MYCOBACTERIUM SMEGMATIS, ALS COLLABORATIVE CRYSTALLOGRAPHY EXPDTA X-RAY DIFFRACTION AUTHOR SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE (SSGCID) REVDAT 4 06-SEP-23 3P4T 1 REMARK SEQADV REVDAT 3 08-NOV-17 3P4T 1 REMARK REVDAT 2 22-APR-15 3P4T 1 JRNL VERSN REVDAT 1 20-OCT-10 3P4T 0 JRNL AUTH L.BAUGH,I.PHAN,D.W.BEGLEY,M.C.CLIFTON,B.ARMOUR,D.M.DRANOW, JRNL AUTH 2 B.M.TAYLOR,M.M.MURUTHI,J.ABENDROTH,J.W.FAIRMAN,D.FOX, JRNL AUTH 3 S.H.DIETERICH,B.L.STAKER,A.S.GARDBERG,R.CHOI,S.N.HEWITT, JRNL AUTH 4 A.J.NAPULI,J.MYERS,L.K.BARRETT,Y.ZHANG,M.FERRELL,E.MUNDT, JRNL AUTH 5 K.THOMPKINS,N.TRAN,S.LYONS-ABBOTT,A.ABRAMOV,A.SEKAR, JRNL AUTH 6 D.SERBZHINSKIY,D.LORIMER,G.W.BUCHKO,R.STACY,L.J.STEWART, JRNL AUTH 7 T.E.EDWARDS,W.C.VAN VOORHIS,P.J.MYLER JRNL TITL INCREASING THE STRUCTURAL COVERAGE OF TUBERCULOSIS DRUG JRNL TITL 2 TARGETS. JRNL REF TUBERCULOSIS (EDINB) V. 95 142 2015 JRNL REFN ISSN 1472-9792 JRNL PMID 25613812 JRNL DOI 10.1016/J.TUBE.2014.12.003 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.82 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 85373 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) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4271 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5822 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.2060 REMARK 3 BIN FREE R VALUE SET COUNT : 308 REMARK 3 BIN FREE R VALUE : 0.2470 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5704 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 114 REMARK 3 SOLVENT ATOMS : 780 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.80000 REMARK 3 B22 (A**2) : 0.51000 REMARK 3 B33 (A**2) : 0.16000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.16000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.094 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.093 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.055 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.653 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6048 ; 0.015 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 4059 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8245 ; 1.563 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9822 ; 1.026 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 796 ; 5.354 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 269 ;34.682 ;22.677 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 944 ;11.821 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 64 ;18.496 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 921 ; 0.109 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6922 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1290 ; 0.001 ; 0.020 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): 3794 ; 0.814 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1610 ; 0.250 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6053 ; 1.446 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2254 ; 2.350 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2174 ; 3.788 ; 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A -10 A 9999 REMARK 3 ORIGIN FOR THE GROUP (A): 0.0410 38.7110 59.3370 REMARK 3 T TENSOR REMARK 3 T11: 0.0587 T22: 0.1120 REMARK 3 T33: 0.0094 T12: 0.0142 REMARK 3 T13: -0.0139 T23: -0.0055 REMARK 3 L TENSOR REMARK 3 L11: 0.6034 L22: 0.3522 REMARK 3 L33: 0.3696 L12: -0.0833 REMARK 3 L13: 0.0781 L23: -0.1554 REMARK 3 S TENSOR REMARK 3 S11: -0.0207 S12: -0.0658 S13: -0.0105 REMARK 3 S21: 0.0248 S22: 0.0339 S23: 0.0330 REMARK 3 S31: 0.0125 S32: -0.0022 S33: -0.0132 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B -10 B 9999 REMARK 3 ORIGIN FOR THE GROUP (A): 7.2990 51.9730 26.2580 REMARK 3 T TENSOR REMARK 3 T11: 0.0453 T22: 0.1155 REMARK 3 T33: 0.0197 T12: -0.0246 REMARK 3 T13: -0.0117 T23: -0.0110 REMARK 3 L TENSOR REMARK 3 L11: 0.9871 L22: 0.3535 REMARK 3 L33: 0.3829 L12: 0.1122 REMARK 3 L13: 0.0097 L23: -0.0627 REMARK 3 S TENSOR REMARK 3 S11: -0.0277 S12: 0.0523 S13: 0.1029 REMARK 3 S21: -0.0305 S22: 0.0493 S23: 0.0019 REMARK 3 S31: -0.0263 S32: 0.0506 S33: -0.0216 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 REMARK 4 REMARK 4 3P4T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-OCT-10. REMARK 100 THE DEPOSITION ID IS D_1000061956. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUN-10 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.5 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) : 1.000 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 85434 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.6800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.20900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: DIRECT FROM 3OIB REMARK 200 STARTING MODEL: PDB ENTRY 3OIB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: EBS PACT SCEEN F12: 0.2M SODIUM REMARK 280 MALONATE, 0.1M BIS TRIS PROPANE PH 6.5; MYSMA.00247.B.A1 PW28486 REMARK 280 AT 27MG/ML, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 290K, VAPOR DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 80.96500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.37500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 80.96500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 32.37500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 20360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 49830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -68.0 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 -31.45002 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 77.68534 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 1 REMARK 465 ALA A 2 REMARK 465 HIS A 3 REMARK 465 HIS A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 MET A 9 REMARK 465 GLY A 10 REMARK 465 THR A 11 REMARK 465 LEU A 12 REMARK 465 GLU A 13 REMARK 465 ALA A 14 REMARK 465 GLN A 15 REMARK 465 THR A 16 REMARK 465 GLN A 17 REMARK 465 GLY A 18 REMARK 465 PRO A 19 REMARK 465 GLY A 20 REMARK 465 SER A 21 REMARK 465 MET A 22 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 HIS B 3 REMARK 465 HIS B 4 REMARK 465 HIS B 5 REMARK 465 HIS B 6 REMARK 465 HIS B 7 REMARK 465 HIS B 8 REMARK 465 MET B 9 REMARK 465 GLY B 10 REMARK 465 THR B 11 REMARK 465 LEU B 12 REMARK 465 GLU B 13 REMARK 465 ALA B 14 REMARK 465 GLN B 15 REMARK 465 THR B 16 REMARK 465 GLN B 17 REMARK 465 GLY B 18 REMARK 465 PRO B 19 REMARK 465 GLY B 20 REMARK 465 SER B 21 REMARK 465 MET B 22 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 ARG A 162 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 35 CG CD CE NZ REMARK 470 ARG B 160 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 162 CG CD NE CZ NH1 NH2 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 OE1 GLU A 347 O HOH A 695 2.10 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 226 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 226 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 312 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAO B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAO A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2OIB RELATED DB: PDB REMARK 900 MYSMA.00247.B.A1, IODIDE SOAK USED FOR PHASING REMARK 900 RELATED ID: MYSMA.00247.B RELATED DB: TARGETDB DBREF 3P4T A 22 403 UNP A0R3J1 A0R3J1_MYCS2 1 382 DBREF 3P4T B 22 403 UNP A0R3J1 A0R3J1_MYCS2 1 382 SEQADV 3P4T MET A 1 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T ALA A 2 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T HIS A 3 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T HIS A 4 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T HIS A 5 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T HIS A 6 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T HIS A 7 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T HIS A 8 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T MET A 9 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T GLY A 10 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T THR A 11 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T LEU A 12 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T GLU A 13 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T ALA A 14 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T GLN A 15 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T THR A 16 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T GLN A 17 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T GLY A 18 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T PRO A 19 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T GLY A 20 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T SER A 21 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T MET B 1 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T ALA B 2 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T HIS B 3 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T HIS B 4 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T HIS B 5 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T HIS B 6 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T HIS B 7 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T HIS B 8 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T MET B 9 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T GLY B 10 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T THR B 11 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T LEU B 12 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T GLU B 13 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T ALA B 14 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T GLN B 15 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T THR B 16 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T GLN B 17 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T GLY B 18 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T PRO B 19 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T GLY B 20 UNP A0R3J1 EXPRESSION TAG SEQADV 3P4T SER B 21 UNP A0R3J1 EXPRESSION TAG SEQRES 1 A 403 MET ALA HIS HIS HIS HIS HIS HIS MET GLY THR LEU GLU SEQRES 2 A 403 ALA GLN THR GLN GLY PRO GLY SER MET SER ILE TRP THR SEQRES 3 A 403 THR ALA GLU ARG GLU ALA LEU ARG LYS THR VAL ARG ALA SEQRES 4 A 403 PHE ALA GLU ARG GLU VAL LEU PRO HIS ALA HIS GLU TRP SEQRES 5 A 403 GLU ARG ALA GLY GLU ILE PRO ARG GLU LEU HIS ARG LYS SEQRES 6 A 403 ALA ALA GLU LEU GLY LEU LEU GLY ALA GLY PHE PRO GLU SEQRES 7 A 403 ASP ALA GLY GLY SER GLY GLY ASP GLY ALA ASP PRO VAL SEQRES 8 A 403 VAL ILE CYS GLU GLU MET HIS TYR ALA GLY SER PRO GLY SEQRES 9 A 403 GLY VAL TYR ALA SER LEU PHE THR CYS GLY ILE ALA VAL SEQRES 10 A 403 PRO HIS MET ILE ALA SER GLY ASP GLN ARG LEU ILE ASP SEQRES 11 A 403 THR TYR VAL ARG PRO THR LEU ARG GLY GLU LYS ILE GLY SEQRES 12 A 403 ALA LEU ALA ILE THR GLU PRO GLY GLY GLY SER ASP VAL SEQRES 13 A 403 GLY HIS LEU ARG THR ARG ALA ASP LEU ASP GLY ASP HIS SEQRES 14 A 403 TYR VAL ILE ASN GLY ALA LYS THR TYR ILE THR SER GLY SEQRES 15 A 403 VAL ARG ALA ASP TYR VAL VAL THR ALA ALA ARG THR GLY SEQRES 16 A 403 GLY PRO GLY ALA GLY GLY VAL SER LEU ILE VAL VAL ASP SEQRES 17 A 403 LYS GLY THR PRO GLY PHE GLU VAL THR ARG LYS LEU ASP SEQRES 18 A 403 LYS MET GLY TRP ARG SER SER ASP THR ALA GLU LEU SER SEQRES 19 A 403 TYR THR ASP VAL ARG VAL PRO VAL ALA ASN LEU VAL GLY SEQRES 20 A 403 SER GLU ASN THR GLY PHE ALA GLN ILE ALA ALA ALA PHE SEQRES 21 A 403 VAL ALA GLU ARG VAL GLY LEU ALA THR GLN ALA TYR ALA SEQRES 22 A 403 GLY ALA GLN ARG CYS LEU ASP LEU THR VAL GLU TRP CYS SEQRES 23 A 403 ARG ASN ARG ASP THR PHE GLY ARG PRO LEU ILE SER ARG SEQRES 24 A 403 GLN ALA VAL GLN ASN THR LEU ALA GLY MET ALA ARG ARG SEQRES 25 A 403 ILE ASP VAL ALA ARG VAL TYR THR ARG HIS VAL VAL GLU SEQRES 26 A 403 ARG GLN LEU ALA GLY GLU THR ASN LEU ILE ALA GLU VAL SEQRES 27 A 403 CYS PHE ALA LYS ASN THR ALA VAL GLU ALA GLY GLU TRP SEQRES 28 A 403 VAL ALA ASN GLN ALA VAL GLN LEU PHE GLY GLY MET GLY SEQRES 29 A 403 TYR MET ALA GLU SER GLU VAL GLU ARG GLN TYR ARG ASP SEQRES 30 A 403 MET ARG ILE LEU GLY ILE GLY GLY GLY THR THR GLU ILE SEQRES 31 A 403 LEU THR SER LEU ALA ALA LYS THR LEU GLY PHE GLN SER SEQRES 1 B 403 MET ALA HIS HIS HIS HIS HIS HIS MET GLY THR LEU GLU SEQRES 2 B 403 ALA GLN THR GLN GLY PRO GLY SER MET SER ILE TRP THR SEQRES 3 B 403 THR ALA GLU ARG GLU ALA LEU ARG LYS THR VAL ARG ALA SEQRES 4 B 403 PHE ALA GLU ARG GLU VAL LEU PRO HIS ALA HIS GLU TRP SEQRES 5 B 403 GLU ARG ALA GLY GLU ILE PRO ARG GLU LEU HIS ARG LYS SEQRES 6 B 403 ALA ALA GLU LEU GLY LEU LEU GLY ALA GLY PHE PRO GLU SEQRES 7 B 403 ASP ALA GLY GLY SER GLY GLY ASP GLY ALA ASP PRO VAL SEQRES 8 B 403 VAL ILE CYS GLU GLU MET HIS TYR ALA GLY SER PRO GLY SEQRES 9 B 403 GLY VAL TYR ALA SER LEU PHE THR CYS GLY ILE ALA VAL SEQRES 10 B 403 PRO HIS MET ILE ALA SER GLY ASP GLN ARG LEU ILE ASP SEQRES 11 B 403 THR TYR VAL ARG PRO THR LEU ARG GLY GLU LYS ILE GLY SEQRES 12 B 403 ALA LEU ALA ILE THR GLU PRO GLY GLY GLY SER ASP VAL SEQRES 13 B 403 GLY HIS LEU ARG THR ARG ALA ASP LEU ASP GLY ASP HIS SEQRES 14 B 403 TYR VAL ILE ASN GLY ALA LYS THR TYR ILE THR SER GLY SEQRES 15 B 403 VAL ARG ALA ASP TYR VAL VAL THR ALA ALA ARG THR GLY SEQRES 16 B 403 GLY PRO GLY ALA GLY GLY VAL SER LEU ILE VAL VAL ASP SEQRES 17 B 403 LYS GLY THR PRO GLY PHE GLU VAL THR ARG LYS LEU ASP SEQRES 18 B 403 LYS MET GLY TRP ARG SER SER ASP THR ALA GLU LEU SER SEQRES 19 B 403 TYR THR ASP VAL ARG VAL PRO VAL ALA ASN LEU VAL GLY SEQRES 20 B 403 SER GLU ASN THR GLY PHE ALA GLN ILE ALA ALA ALA PHE SEQRES 21 B 403 VAL ALA GLU ARG VAL GLY LEU ALA THR GLN ALA TYR ALA SEQRES 22 B 403 GLY ALA GLN ARG CYS LEU ASP LEU THR VAL GLU TRP CYS SEQRES 23 B 403 ARG ASN ARG ASP THR PHE GLY ARG PRO LEU ILE SER ARG SEQRES 24 B 403 GLN ALA VAL GLN ASN THR LEU ALA GLY MET ALA ARG ARG SEQRES 25 B 403 ILE ASP VAL ALA ARG VAL TYR THR ARG HIS VAL VAL GLU SEQRES 26 B 403 ARG GLN LEU ALA GLY GLU THR ASN LEU ILE ALA GLU VAL SEQRES 27 B 403 CYS PHE ALA LYS ASN THR ALA VAL GLU ALA GLY GLU TRP SEQRES 28 B 403 VAL ALA ASN GLN ALA VAL GLN LEU PHE GLY GLY MET GLY SEQRES 29 B 403 TYR MET ALA GLU SER GLU VAL GLU ARG GLN TYR ARG ASP SEQRES 30 B 403 MET ARG ILE LEU GLY ILE GLY GLY GLY THR THR GLU ILE SEQRES 31 B 403 LEU THR SER LEU ALA ALA LYS THR LEU GLY PHE GLN SER HET EDO A 501 4 HET FAO A 500 53 HET FAO B 500 53 HET EDO B 501 4 HETNAM EDO 1,2-ETHANEDIOL HETNAM FAO [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4- HETNAM 2 FAO DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL (2R,3S,4S)-5- HETNAM 3 FAO [(4AS,10AR)-7,8-DIMETHYL-2,4-DIOXO-1,3,4,4A,5,10A- HETNAM 4 FAO HEXAHYDROBENZO[G]PTERIDIN-10(2H)-YL]-2,3,4- HETNAM 5 FAO TRIHYDROXYPENTYL DIHYDROGEN DIPHOSPHATE HETSYN EDO ETHYLENE GLYCOL FORMUL 3 EDO 2(C2 H6 O2) FORMUL 4 FAO 2(C27 H37 N9 O15 P2) FORMUL 7 HOH *780(H2 O) HELIX 1 1 THR A 27 VAL A 45 1 19 HELIX 2 2 HIS A 48 GLY A 56 1 9 HELIX 3 3 PRO A 59 LEU A 69 1 11 HELIX 4 4 PRO A 77 GLY A 81 5 5 HELIX 5 5 GLY A 87 ALA A 100 1 14 HELIX 6 6 PRO A 103 PHE A 111 1 9 HELIX 7 7 THR A 112 VAL A 117 1 6 HELIX 8 8 VAL A 117 GLY A 124 1 8 HELIX 9 9 ASP A 125 TYR A 132 1 8 HELIX 10 10 TYR A 132 ARG A 138 1 7 HELIX 11 11 ASP A 155 LEU A 159 5 5 HELIX 12 12 GLY A 198 GLY A 200 5 3 HELIX 13 13 THR A 251 ARG A 289 1 39 HELIX 14 14 ARG A 299 ALA A 329 1 31 HELIX 15 15 LEU A 334 GLY A 361 1 28 HELIX 16 16 GLY A 362 MET A 366 5 5 HELIX 17 17 SER A 369 ARG A 379 1 11 HELIX 18 18 THR A 387 GLY A 400 1 14 HELIX 19 19 THR B 27 VAL B 45 1 19 HELIX 20 20 HIS B 48 GLY B 56 1 9 HELIX 21 21 PRO B 59 LEU B 69 1 11 HELIX 22 22 PRO B 77 GLY B 81 5 5 HELIX 23 23 GLY B 87 ALA B 100 1 14 HELIX 24 24 PRO B 103 PHE B 111 1 9 HELIX 25 25 THR B 112 VAL B 117 1 6 HELIX 26 26 VAL B 117 GLY B 124 1 8 HELIX 27 27 ASP B 125 TYR B 132 1 8 HELIX 28 28 TYR B 132 ARG B 138 1 7 HELIX 29 29 ASP B 155 LEU B 159 5 5 HELIX 30 30 GLY B 198 GLY B 200 5 3 HELIX 31 31 THR B 251 ARG B 289 1 39 HELIX 32 32 ARG B 299 ALA B 329 1 31 HELIX 33 33 LEU B 334 GLY B 361 1 28 HELIX 34 34 GLY B 362 MET B 366 5 5 HELIX 35 35 SER B 369 ARG B 379 1 11 HELIX 36 36 THR B 387 GLY B 400 1 14 SHEET 1 A 4 GLY A 143 ALA A 146 0 SHEET 2 A 4 TYR A 187 ARG A 193 1 O VAL A 189 N ALA A 146 SHEET 3 A 4 VAL A 202 ASP A 208 -1 O ILE A 205 N THR A 190 SHEET 4 A 4 LEU A 245 VAL A 246 -1 O VAL A 246 N LEU A 204 SHEET 1 B 4 ARG A 162 ASP A 166 0 SHEET 2 B 4 HIS A 169 THR A 180 -1 O HIS A 169 N ASP A 166 SHEET 3 B 4 THR A 230 PRO A 241 -1 O LEU A 233 N LYS A 176 SHEET 4 B 4 PHE A 214 LYS A 219 -1 N GLU A 215 O SER A 234 SHEET 1 C 2 ASP A 290 THR A 291 0 SHEET 2 C 2 ARG A 294 PRO A 295 -1 O ARG A 294 N THR A 291 SHEET 1 D 4 GLY B 143 ALA B 146 0 SHEET 2 D 4 TYR B 187 ARG B 193 1 O VAL B 189 N ALA B 146 SHEET 3 D 4 VAL B 202 ASP B 208 -1 O SER B 203 N ALA B 192 SHEET 4 D 4 LEU B 245 VAL B 246 -1 O VAL B 246 N LEU B 204 SHEET 1 E 4 ARG B 162 ASP B 166 0 SHEET 2 E 4 HIS B 169 THR B 180 -1 O HIS B 169 N ASP B 166 SHEET 3 E 4 THR B 230 PRO B 241 -1 O VAL B 240 N TYR B 170 SHEET 4 E 4 PHE B 214 LYS B 219 -1 N GLU B 215 O SER B 234 SHEET 1 F 2 ASP B 290 THR B 291 0 SHEET 2 F 2 ARG B 294 PRO B 295 -1 O ARG B 294 N THR B 291 SITE 1 AC1 31 ARG A 289 THR A 291 LEU A 296 ARG A 299 SITE 2 AC1 31 GLN A 300 GLN A 358 LEU A 359 GLY A 361 SITE 3 AC1 31 GLY A 362 LEU B 145 ILE B 147 THR B 148 SITE 4 AC1 31 GLY B 152 GLY B 153 SER B 154 TYR B 178 SITE 5 AC1 31 ILE B 179 THR B 180 LYS B 222 ILE B 380 SITE 6 AC1 31 ILE B 383 THR B 387 GLU B 389 HOH B 411 SITE 7 AC1 31 HOH B 416 HOH B 430 HOH B 434 HOH B 454 SITE 8 AC1 31 HOH B 514 HOH B 610 HOH B 673 SITE 1 AC2 6 GLN A 276 ALA A 310 ARG A 317 HOH A 408 SITE 2 AC2 6 HOH A 786 LEU B 399 SITE 1 AC3 32 LEU A 145 ILE A 147 THR A 148 GLY A 152 SITE 2 AC3 32 GLY A 153 SER A 154 TYR A 178 ILE A 179 SITE 3 AC3 32 THR A 180 LYS A 222 ILE A 380 ILE A 383 SITE 4 AC3 32 THR A 387 GLU A 389 HOH A 416 HOH A 463 SITE 5 AC3 32 HOH A 530 HOH A 575 HOH A 590 HOH A 608 SITE 6 AC3 32 HOH A 618 HOH A 686 ARG B 289 THR B 291 SITE 7 AC3 32 LEU B 296 ARG B 299 GLN B 300 GLN B 358 SITE 8 AC3 32 LEU B 359 GLY B 361 GLY B 362 HOH B 490 SITE 1 AC4 6 LEU A 399 GLN B 276 ALA B 310 ARG B 317 SITE 2 AC4 6 HOH B 842 HOH B 843 CRYST1 161.930 64.750 83.810 90.00 112.04 90.00 C 1 2 1 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 0.006176 0.000000 0.002500 0.00000 SCALE2 0.000000 0.015444 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012873 0.00000