HEADER DNA BINDING PROTEIN 10-NOV-17 5YRX TITLE CRYSTAL STRUCTURE OF A HYPOTHETICAL PROTEIN RV3716C FROM MYCOBACTERIUM TITLE 2 TUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOID-ASSOCIATED PROTEIN RV3716C; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS H37RV; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: RV3716C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MTBRV3716, DNA BINDING, METAL ION, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.DEKA,A.GOPALAN,M.PRABHAVATHI,H.S.SAVITHRI,A.RAJA,M.R.N.MURTHY REVDAT 2 22-NOV-23 5YRX 1 LINK REVDAT 1 16-MAY-18 5YRX 0 JRNL AUTH A.GOPALAN,G.DEKA,M.PRABHAVATHI,H.S.SAVITHRI,M.R.N.MURTHY, JRNL AUTH 2 A.RAJA JRNL TITL STRUCTURAL AND BIOPHYSICAL CHARACTERIZATION OF RV3716C, A JRNL TITL 2 HYPOTHETICAL PROTEIN FROM MYCOBACTERIUM TUBERCULOSIS JRNL REF BIOCHEM. BIOPHYS. RES. V. 495 982 2018 JRNL REF 2 COMMUN. JRNL REFN ESSN 1090-2104 JRNL PMID 29154992 JRNL DOI 10.1016/J.BBRC.2017.11.093 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0069 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 9467 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 464 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 692 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1660 REMARK 3 BIN FREE R VALUE SET COUNT : 28 REMARK 3 BIN FREE R VALUE : 0.1530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 482 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 62 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.88 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.31000 REMARK 3 B22 (A**2) : 1.57000 REMARK 3 B33 (A**2) : -1.27000 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): 0.093 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.102 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.055 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.760 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.904 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 500 ; 0.024 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 501 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 675 ; 2.282 ; 1.992 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1145 ; 1.169 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 72 ; 8.188 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 15 ;32.710 ;28.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 79 ;15.229 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 1 ;14.011 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 87 ; 0.159 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 570 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 85 ; 0.002 ; 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): 285 ; 3.439 ; 3.228 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 284 ; 3.407 ; 3.213 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 355 ; 4.774 ; 4.793 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 356 ; 4.777 ; 4.813 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 215 ; 4.902 ; 3.276 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 215 ; 4.906 ; 3.275 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 320 ; 7.057 ; 4.778 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 612 ; 9.208 ;25.398 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 583 ; 9.108 ;24.911 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 : NULL 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 ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5YRX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1300005797. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9968 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 37.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.70 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : 0.03100 REMARK 200 FOR THE DATA SET : 24.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.50 REMARK 200 R MERGE FOR SHELL (I) : 0.22700 REMARK 200 R SYM FOR SHELL (I) : 0.23900 REMARK 200 FOR SHELL : 12.10 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1YBX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20MM SODIUM PHOSPHATE PH 5.5 0.1M REMARK 280 CADMIUM CHLORIDE 0.1M MAGNESIUM CHLORIDE 0.1M NICKEL CHLORIDE 24% REMARK 280 PEG 4000, BATCH MODE, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 18.62500 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 18.62500 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 17.55500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 91.87500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 17.55500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 91.87500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 18.62500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 17.55500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 91.87500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 18.62500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 17.55500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 91.87500 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 -35.11000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 93.12500 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 357 LIES ON A SPECIAL POSITION. 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 -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 GLN A 2 REMARK 465 PRO A 3 REMARK 465 GLY A 4 REMARK 465 GLY A 5 REMARK 465 ASP A 6 REMARK 465 MET A 7 REMARK 465 SER A 8 REMARK 465 ALA A 9 REMARK 465 LEU A 10 REMARK 465 LEU A 11 REMARK 465 ALA A 12 REMARK 465 GLN A 13 REMARK 465 ALA A 14 REMARK 465 GLN A 15 REMARK 465 GLN A 16 REMARK 465 MET A 17 REMARK 465 GLN A 18 REMARK 465 GLN A 19 REMARK 465 LYS A 20 REMARK 465 LEU A 21 REMARK 465 LEU A 93 REMARK 465 GLY A 94 REMARK 465 ALA A 95 REMARK 465 LEU A 96 REMARK 465 ALA A 97 REMARK 465 GLY A 98 REMARK 465 ALA A 99 REMARK 465 MET A 100 REMARK 465 ARG A 101 REMARK 465 PRO A 102 REMARK 465 PRO A 103 REMARK 465 ALA A 104 REMARK 465 PRO A 105 REMARK 465 PRO A 106 REMARK 465 ALA A 107 REMARK 465 ALA A 108 REMARK 465 PRO A 109 REMARK 465 PRO A 110 REMARK 465 GLY A 111 REMARK 465 ALA A 112 REMARK 465 PRO A 113 REMARK 465 GLY A 114 REMARK 465 MET A 115 REMARK 465 PRO A 116 REMARK 465 GLY A 117 REMARK 465 MET A 118 REMARK 465 PRO A 119 REMARK 465 GLY A 120 REMARK 465 MET A 121 REMARK 465 PRO A 122 REMARK 465 GLY A 123 REMARK 465 ALA A 124 REMARK 465 PRO A 125 REMARK 465 GLY A 126 REMARK 465 ALA A 127 REMARK 465 PRO A 128 REMARK 465 PRO A 129 REMARK 465 VAL A 130 REMARK 465 PRO A 131 REMARK 465 GLY A 132 REMARK 465 ILE A 133 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 23 CG CD OE1 OE2 REMARK 470 GLN A 25 CG CD OE1 NE2 REMARK 470 GLN A 26 CG CD OE1 NE2 REMARK 470 GLN A 27 CG CD OE1 NE2 REMARK 470 ASN A 30 CG OD1 ND2 REMARK 470 SER A 31 OG REMARK 470 LYS A 60 NZ REMARK 470 LYS A 87 CG CD CE NZ REMARK 470 GLN A 90 CG CD OE1 NE2 REMARK 470 GLU A 91 CG CD OE1 OE2 REMARK 470 ARG A 92 CG CD NE CZ NH1 NH2 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 GLN A 27 28.09 -75.22 REMARK 500 GLN A 90 72.30 -65.84 REMARK 500 GLU A 91 71.31 -159.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 201 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 58 OD1 REMARK 620 2 ASP A 58 OD2 53.5 REMARK 620 3 GLU A 68 OE2 28.2 68.7 REMARK 620 4 ASP A 72 OD1 30.9 62.8 9.1 REMARK 620 5 ASP A 72 OD2 35.1 69.0 8.4 6.3 REMARK 620 6 EDO A 202 O1 32.7 64.7 9.0 2.1 4.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 204 DBREF 5YRX A 1 133 UNP P9WNR9 Y3716_MYCTU 1 133 SEQADV 5YRX HIS A -5 UNP P9WNR9 EXPRESSION TAG SEQADV 5YRX HIS A -4 UNP P9WNR9 EXPRESSION TAG SEQADV 5YRX HIS A -3 UNP P9WNR9 EXPRESSION TAG SEQADV 5YRX HIS A -2 UNP P9WNR9 EXPRESSION TAG SEQADV 5YRX HIS A -1 UNP P9WNR9 EXPRESSION TAG SEQADV 5YRX HIS A 0 UNP P9WNR9 EXPRESSION TAG SEQRES 1 A 139 HIS HIS HIS HIS HIS HIS MET GLN PRO GLY GLY ASP MET SEQRES 2 A 139 SER ALA LEU LEU ALA GLN ALA GLN GLN MET GLN GLN LYS SEQRES 3 A 139 LEU LEU GLU ALA GLN GLN GLN LEU ALA ASN SER GLU VAL SEQRES 4 A 139 HIS GLY GLN ALA GLY GLY GLY LEU VAL LYS VAL VAL VAL SEQRES 5 A 139 LYS GLY SER GLY GLU VAL ILE GLY VAL THR ILE ASP PRO SEQRES 6 A 139 LYS VAL VAL ASP PRO ASP ASP ILE GLU THR LEU GLN ASP SEQRES 7 A 139 LEU ILE VAL GLY ALA MET ARG ASP ALA SER GLN GLN VAL SEQRES 8 A 139 THR LYS MET ALA GLN GLU ARG LEU GLY ALA LEU ALA GLY SEQRES 9 A 139 ALA MET ARG PRO PRO ALA PRO PRO ALA ALA PRO PRO GLY SEQRES 10 A 139 ALA PRO GLY MET PRO GLY MET PRO GLY MET PRO GLY ALA SEQRES 11 A 139 PRO GLY ALA PRO PRO VAL PRO GLY ILE HET CD A 201 1 HET EDO A 202 4 HET EDO A 203 4 HET EDO A 204 4 HETNAM CD CADMIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 CD CD 2+ FORMUL 3 EDO 3(C2 H6 O2) FORMUL 6 HOH *62(H2 O) HELIX 1 AA1 LEU A 22 GLN A 27 1 6 HELIX 2 AA2 PRO A 59 VAL A 62 5 4 HELIX 3 AA3 ASP A 66 GLN A 90 1 25 SHEET 1 AA1 3 GLU A 32 ALA A 37 0 SHEET 2 AA1 3 VAL A 42 LYS A 47 -1 O VAL A 46 N VAL A 33 SHEET 3 AA1 3 VAL A 52 ILE A 57 -1 O ILE A 53 N VAL A 45 LINK OD1 ASP A 58 CD CD A 201 1555 6354 2.49 LINK OD2 ASP A 58 CD CD A 201 1555 6354 2.35 LINK OE2 GLU A 68 CD CD A 201 1555 1555 2.41 LINK OD1 ASP A 72 CD CD A 201 1555 1555 2.68 LINK OD2 ASP A 72 CD CD A 201 1555 1555 2.23 LINK CD CD A 201 O1 EDO A 202 1555 6355 2.63 SITE 1 AC1 4 ASP A 58 GLU A 68 ASP A 72 EDO A 202 SITE 1 AC2 5 ASP A 58 PRO A 59 LYS A 60 ASP A 72 SITE 2 AC2 5 CD A 201 SITE 1 AC3 7 HIS A 34 GLY A 35 LYS A 43 VAL A 44 SITE 2 AC3 7 VAL A 45 HOH A 303 HOH A 305 SITE 1 AC4 7 GLY A 50 GLU A 51 VAL A 52 MET A 78 SITE 2 AC4 7 ARG A 79 SER A 82 HOH A 320 CRYST1 35.110 183.750 37.250 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 0.028482 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005442 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026846 0.00000