HEADER DNA BINDING PROTEIN/DNA 19-SEP-13 4MTD
TITLE ZINC UPTAKE REGULATOR COMPLEXED WITH ZINC AND DNA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ZINC UPTAKE REGULATION PROTEIN;
COMPND 3 CHAIN: A, B, C, D;
COMPND 4 SYNONYM: ZINC UPTAKE REGULATOR;
COMPND 5 ENGINEERED: YES;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: ZNUABC OPERATOR DNA;
COMPND 8 CHAIN: Y;
COMPND 9 ENGINEERED: YES;
COMPND 10 MOL_ID: 3;
COMPND 11 MOLECULE: ZNUABC OPERATOR DNA;
COMPND 12 CHAIN: Z;
COMPND 13 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 3 ORGANISM_TAXID: 83333;
SOURCE 4 STRAIN: K12;
SOURCE 5 GENE: B4046, JW5714, YJBK, ZUR;
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: PET24D;
SOURCE 11 MOL_ID: 2;
SOURCE 12 SYNTHETIC: YES;
SOURCE 13 MOL_ID: 3;
SOURCE 14 SYNTHETIC: YES
KEYWDS PROTEIN-DNA COMPLEX, WINGED-HELIX, DNA-BINDING REGULATORY PROTEIN,
KEYWDS 2 HELIX-TURN-HELIX, WINGED HELIX, ZINC REGULATED REPRESSOR, DNA
KEYWDS 3 BINDING, DNA BINDING PROTEIN-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR B.A.GILSTON,A.MONDRAGON,T.V.O'HALLORAN
REVDAT 3 28-FEB-24 4MTD 1 REMARK LINK
REVDAT 2 12-NOV-14 4MTD 1 JRNL
REVDAT 1 05-NOV-14 4MTD 0
JRNL AUTH B.A.GILSTON,S.WANG,M.D.MARCUS,M.A.CANALIZO-HERNANDEZ,
JRNL AUTH 2 E.P.SWINDELL,Y.XUE,A.MONDRAGON,T.V.O'HALLORAN
JRNL TITL STRUCTURAL AND MECHANISTIC BASIS OF ZINC REGULATION ACROSS
JRNL TITL 2 THE E. COLI ZUR REGULON.
JRNL REF PLOS BIOL. V. 12 01987 2014
JRNL REFN ISSN 1544-9173
JRNL PMID 25369000
JRNL DOI 10.1371/JOURNAL.PBIO.1001987
REMARK 2
REMARK 2 RESOLUTION. 2.50 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.6.0117
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) : 36.34
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 3 NUMBER OF REFLECTIONS : 43139
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) : 0.236
REMARK 3 R VALUE (WORKING SET) : 0.234
REMARK 3 FREE R VALUE : 0.271
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 2290
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) : 2.57
REMARK 3 REFLECTION IN BIN (WORKING SET) : 3120
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.34
REMARK 3 BIN R VALUE (WORKING SET) : 0.3090
REMARK 3 BIN FREE R VALUE SET COUNT : 141
REMARK 3 BIN FREE R VALUE : 0.3210
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4632
REMARK 3 NUCLEIC ACID ATOMS : 1355
REMARK 3 HETEROGEN ATOMS : 8
REMARK 3 SOLVENT ATOMS : 0
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 64.42
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 5.20000
REMARK 3 B22 (A**2) : -2.84000
REMARK 3 B33 (A**2) : -1.45000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.06000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.334
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.258
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.198
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.890
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.913
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6263 ; 0.006 ; 0.017
REMARK 3 BOND LENGTHS OTHERS (A): 5328 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8742 ; 1.117 ; 1.763
REMARK 3 BOND ANGLES OTHERS (DEGREES): 12290 ; 0.896 ; 3.003
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 596 ; 6.342 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 218 ;32.824 ;24.404
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 832 ;14.167 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;12.306 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 948 ; 0.063 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6175 ; 0.005 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 1339 ; 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): 2390 ; 2.748 ; 6.306
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2389 ; 2.748 ; 6.304
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2981 ; 4.637 ; 9.446
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3873 ; 3.181 ; 6.693
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
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 4MTD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-NOV-13.
REMARK 100 THE DEPOSITION ID IS D_1000082340.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 07-FEB-11
REMARK 200 TEMPERATURE (KELVIN) : 78
REMARK 200 PH : 5.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 21-ID-F
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872
REMARK 200 MONOCHROMATOR : GRAPHITE
REMARK 200 OPTICS : BERYLLIUM LENSES
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XDS, SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45429
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.480
REMARK 200 RESOLUTION RANGE LOW (A) : 36.400
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 200 DATA REDUNDANCY : 4.100
REMARK 200 R MERGE (I) : 0.04600
REMARK 200 R SYM (I) : 0.05400
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.4000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.48
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.61
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0
REMARK 200 DATA REDUNDANCY IN SHELL : 4.20
REMARK 200 R MERGE FOR SHELL (I) : 0.29000
REMARK 200 R SYM FOR SHELL (I) : 0.33100
REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.000
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: SHARP
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 64.37
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.45
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M AMMONIUM SULFATE, 0.1 M CITRATE,
REMARK 280 PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K
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 96.66200
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.23500
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 96.66200
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 40.23500
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 300 REMARK: A DIMER OF DIMERS IS COMPLEXED WITH THE DUPLEX DNA MOLECULE.
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: HEXAMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 15130 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 38870 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -110.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, Y, Z
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 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 GLU A 2
REMARK 465 LYS A 3
REMARK 465 ARG A 153
REMARK 465 HIS A 154
REMARK 465 PRO A 155
REMARK 465 GLU A 156
REMARK 465 GLN A 157
REMARK 465 CYS A 158
REMARK 465 GLN A 159
REMARK 465 HIS A 160
REMARK 465 ASP A 161
REMARK 465 HIS A 162
REMARK 465 SER A 163
REMARK 465 VAL A 164
REMARK 465 GLN A 165
REMARK 465 VAL A 166
REMARK 465 LYS A 167
REMARK 465 LYS A 168
REMARK 465 LYS A 169
REMARK 465 PRO A 170
REMARK 465 ARG A 171
REMARK 465 MET B 1
REMARK 465 GLU B 2
REMARK 465 ARG B 153
REMARK 465 HIS B 154
REMARK 465 PRO B 155
REMARK 465 GLU B 156
REMARK 465 GLN B 157
REMARK 465 CYS B 158
REMARK 465 GLN B 159
REMARK 465 HIS B 160
REMARK 465 ASP B 161
REMARK 465 HIS B 162
REMARK 465 SER B 163
REMARK 465 VAL B 164
REMARK 465 GLN B 165
REMARK 465 VAL B 166
REMARK 465 LYS B 167
REMARK 465 LYS B 168
REMARK 465 LYS B 169
REMARK 465 PRO B 170
REMARK 465 ARG B 171
REMARK 465 MET C 1
REMARK 465 GLU C 2
REMARK 465 LYS C 3
REMARK 465 THR C 4
REMARK 465 ARG C 153
REMARK 465 HIS C 154
REMARK 465 PRO C 155
REMARK 465 GLU C 156
REMARK 465 GLN C 157
REMARK 465 CYS C 158
REMARK 465 GLN C 159
REMARK 465 HIS C 160
REMARK 465 ASP C 161
REMARK 465 HIS C 162
REMARK 465 SER C 163
REMARK 465 VAL C 164
REMARK 465 GLN C 165
REMARK 465 VAL C 166
REMARK 465 LYS C 167
REMARK 465 LYS C 168
REMARK 465 LYS C 169
REMARK 465 PRO C 170
REMARK 465 ARG C 171
REMARK 465 MET D 1
REMARK 465 ARG D 153
REMARK 465 HIS D 154
REMARK 465 PRO D 155
REMARK 465 GLU D 156
REMARK 465 GLN D 157
REMARK 465 CYS D 158
REMARK 465 GLN D 159
REMARK 465 HIS D 160
REMARK 465 ASP D 161
REMARK 465 HIS D 162
REMARK 465 SER D 163
REMARK 465 VAL D 164
REMARK 465 GLN D 165
REMARK 465 VAL D 166
REMARK 465 LYS D 167
REMARK 465 LYS D 168
REMARK 465 LYS D 169
REMARK 465 PRO D 170
REMARK 465 ARG D 171
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
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 RES CSSEQI ATM2 DEVIATION
REMARK 500 DA Y 1 P DA Y 1 OP3 -0.122
REMARK 500 DT Z 1 P DT Z 1 OP3 -0.121
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 ASN A 83 83.24 -68.24
REMARK 500 PHE A 91 -80.36 -67.32
REMARK 500 PRO B 94 -142.97 -75.98
REMARK 500 ALA B 114 77.89 -168.60
REMARK 500 ASP C 39 54.28 -98.71
REMARK 500 GLN C 73 -159.88 -72.94
REMARK 500 THR C 95 111.98 -38.87
REMARK 500 ASN D 21 67.28 -108.40
REMARK 500 ASP D 39 37.73 -92.32
REMARK 500 LEU D 90 25.41 -145.19
REMARK 500 THR D 95 150.87 -49.75
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 ZN A 202 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 77 NE2
REMARK 620 2 CYS A 88 SG 104.4
REMARK 620 3 HIS A 96 NE2 107.4 114.4
REMARK 620 4 GLU A 111 OE1 99.7 136.2 91.8
REMARK 620 5 GLU A 111 OE2 90.4 89.2 144.6 54.4
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 201 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 103 SG
REMARK 620 2 CYS A 106 SG 101.3
REMARK 620 3 CYS A 143 SG 122.0 114.3
REMARK 620 4 CYS A 146 SG 102.4 106.6 108.7
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN B 201 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS B 77 NE2
REMARK 620 2 CYS B 88 SG 107.0
REMARK 620 3 HIS B 96 NE2 107.7 111.3
REMARK 620 4 GLU B 111 OE1 88.3 145.5 92.2
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN B 202 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS B 103 SG
REMARK 620 2 CYS B 106 SG 98.6
REMARK 620 3 CYS B 143 SG 119.6 105.4
REMARK 620 4 CYS B 146 SG 85.8 111.8 130.7
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN C 202 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS C 77 NE2
REMARK 620 2 CYS C 88 SG 110.8
REMARK 620 3 HIS C 96 NE2 104.3 101.9
REMARK 620 4 GLU C 111 OE1 102.2 140.9 89.3
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN C 201 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS C 103 SG
REMARK 620 2 CYS C 106 SG 108.2
REMARK 620 3 CYS C 143 SG 110.1 109.7
REMARK 620 4 CYS C 146 SG 97.6 121.8 108.6
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN D 202 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS D 77 NE2
REMARK 620 2 CYS D 88 SG 105.8
REMARK 620 3 HIS D 96 NE2 109.3 107.4
REMARK 620 4 GLU D 111 OE1 95.6 144.8 90.8
REMARK 620 5 GLU D 111 OE2 106.2 92.7 131.9 54.1
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN D 201 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS D 103 SG
REMARK 620 2 CYS D 106 SG 102.4
REMARK 620 3 CYS D 143 SG 120.2 105.8
REMARK 620 4 CYS D 146 SG 86.1 105.6 132.6
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 202
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 202
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 202
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D 202
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4MTE RELATED DB: PDB
DBREF 4MTD A 1 171 UNP P0AC51 ZUR_ECOLI 1 171
DBREF 4MTD B 1 171 UNP P0AC51 ZUR_ECOLI 1 171
DBREF 4MTD C 1 171 UNP P0AC51 ZUR_ECOLI 1 171
DBREF 4MTD D 1 171 UNP P0AC51 ZUR_ECOLI 1 171
DBREF 4MTD Y 1 33 PDB 4MTD 4MTD 1 33
DBREF 4MTD Z 1 33 PDB 4MTD 4MTD 1 33
SEQRES 1 A 171 MET GLU LYS THR THR THR GLN GLU LEU LEU ALA GLN ALA
SEQRES 2 A 171 GLU LYS ILE CYS ALA GLN ARG ASN VAL ARG LEU THR PRO
SEQRES 3 A 171 GLN ARG LEU GLU VAL LEU ARG LEU MET SER LEU GLN ASP
SEQRES 4 A 171 GLY ALA ILE SER ALA TYR ASP LEU LEU ASP LEU LEU ARG
SEQRES 5 A 171 GLU ALA GLU PRO GLN ALA LYS PRO PRO THR VAL TYR ARG
SEQRES 6 A 171 ALA LEU ASP PHE LEU LEU GLU GLN GLY PHE VAL HIS LYS
SEQRES 7 A 171 VAL GLU SER THR ASN SER TYR VAL LEU CYS HIS LEU PHE
SEQRES 8 A 171 ASP GLN PRO THR HIS THR SER ALA MET PHE ILE CYS ASP
SEQRES 9 A 171 ARG CYS GLY ALA VAL LYS GLU GLU CYS ALA GLU GLY VAL
SEQRES 10 A 171 GLU ASP ILE MET HIS THR LEU ALA ALA LYS MET GLY PHE
SEQRES 11 A 171 ALA LEU ARG HIS ASN VAL ILE GLU ALA HIS GLY LEU CYS
SEQRES 12 A 171 ALA ALA CYS VAL GLU VAL GLU ALA CYS ARG HIS PRO GLU
SEQRES 13 A 171 GLN CYS GLN HIS ASP HIS SER VAL GLN VAL LYS LYS LYS
SEQRES 14 A 171 PRO ARG
SEQRES 1 B 171 MET GLU LYS THR THR THR GLN GLU LEU LEU ALA GLN ALA
SEQRES 2 B 171 GLU LYS ILE CYS ALA GLN ARG ASN VAL ARG LEU THR PRO
SEQRES 3 B 171 GLN ARG LEU GLU VAL LEU ARG LEU MET SER LEU GLN ASP
SEQRES 4 B 171 GLY ALA ILE SER ALA TYR ASP LEU LEU ASP LEU LEU ARG
SEQRES 5 B 171 GLU ALA GLU PRO GLN ALA LYS PRO PRO THR VAL TYR ARG
SEQRES 6 B 171 ALA LEU ASP PHE LEU LEU GLU GLN GLY PHE VAL HIS LYS
SEQRES 7 B 171 VAL GLU SER THR ASN SER TYR VAL LEU CYS HIS LEU PHE
SEQRES 8 B 171 ASP GLN PRO THR HIS THR SER ALA MET PHE ILE CYS ASP
SEQRES 9 B 171 ARG CYS GLY ALA VAL LYS GLU GLU CYS ALA GLU GLY VAL
SEQRES 10 B 171 GLU ASP ILE MET HIS THR LEU ALA ALA LYS MET GLY PHE
SEQRES 11 B 171 ALA LEU ARG HIS ASN VAL ILE GLU ALA HIS GLY LEU CYS
SEQRES 12 B 171 ALA ALA CYS VAL GLU VAL GLU ALA CYS ARG HIS PRO GLU
SEQRES 13 B 171 GLN CYS GLN HIS ASP HIS SER VAL GLN VAL LYS LYS LYS
SEQRES 14 B 171 PRO ARG
SEQRES 1 C 171 MET GLU LYS THR THR THR GLN GLU LEU LEU ALA GLN ALA
SEQRES 2 C 171 GLU LYS ILE CYS ALA GLN ARG ASN VAL ARG LEU THR PRO
SEQRES 3 C 171 GLN ARG LEU GLU VAL LEU ARG LEU MET SER LEU GLN ASP
SEQRES 4 C 171 GLY ALA ILE SER ALA TYR ASP LEU LEU ASP LEU LEU ARG
SEQRES 5 C 171 GLU ALA GLU PRO GLN ALA LYS PRO PRO THR VAL TYR ARG
SEQRES 6 C 171 ALA LEU ASP PHE LEU LEU GLU GLN GLY PHE VAL HIS LYS
SEQRES 7 C 171 VAL GLU SER THR ASN SER TYR VAL LEU CYS HIS LEU PHE
SEQRES 8 C 171 ASP GLN PRO THR HIS THR SER ALA MET PHE ILE CYS ASP
SEQRES 9 C 171 ARG CYS GLY ALA VAL LYS GLU GLU CYS ALA GLU GLY VAL
SEQRES 10 C 171 GLU ASP ILE MET HIS THR LEU ALA ALA LYS MET GLY PHE
SEQRES 11 C 171 ALA LEU ARG HIS ASN VAL ILE GLU ALA HIS GLY LEU CYS
SEQRES 12 C 171 ALA ALA CYS VAL GLU VAL GLU ALA CYS ARG HIS PRO GLU
SEQRES 13 C 171 GLN CYS GLN HIS ASP HIS SER VAL GLN VAL LYS LYS LYS
SEQRES 14 C 171 PRO ARG
SEQRES 1 D 171 MET GLU LYS THR THR THR GLN GLU LEU LEU ALA GLN ALA
SEQRES 2 D 171 GLU LYS ILE CYS ALA GLN ARG ASN VAL ARG LEU THR PRO
SEQRES 3 D 171 GLN ARG LEU GLU VAL LEU ARG LEU MET SER LEU GLN ASP
SEQRES 4 D 171 GLY ALA ILE SER ALA TYR ASP LEU LEU ASP LEU LEU ARG
SEQRES 5 D 171 GLU ALA GLU PRO GLN ALA LYS PRO PRO THR VAL TYR ARG
SEQRES 6 D 171 ALA LEU ASP PHE LEU LEU GLU GLN GLY PHE VAL HIS LYS
SEQRES 7 D 171 VAL GLU SER THR ASN SER TYR VAL LEU CYS HIS LEU PHE
SEQRES 8 D 171 ASP GLN PRO THR HIS THR SER ALA MET PHE ILE CYS ASP
SEQRES 9 D 171 ARG CYS GLY ALA VAL LYS GLU GLU CYS ALA GLU GLY VAL
SEQRES 10 D 171 GLU ASP ILE MET HIS THR LEU ALA ALA LYS MET GLY PHE
SEQRES 11 D 171 ALA LEU ARG HIS ASN VAL ILE GLU ALA HIS GLY LEU CYS
SEQRES 12 D 171 ALA ALA CYS VAL GLU VAL GLU ALA CYS ARG HIS PRO GLU
SEQRES 13 D 171 GLN CYS GLN HIS ASP HIS SER VAL GLN VAL LYS LYS LYS
SEQRES 14 D 171 PRO ARG
SEQRES 1 Y 33 DA DG DA DA DG DT DG DT DG DA DT DA DT
SEQRES 2 Y 33 DT DA DT DA DA DC DA DT DT DT DC DA DT
SEQRES 3 Y 33 DG DA DC DT DA DT DG
SEQRES 1 Z 33 DT DA DG DT DC DA DT DG DA DA DA DT DG
SEQRES 2 Z 33 DT DT DA DT DA DA DT DA DT DC DA DC DA
SEQRES 3 Z 33 DC DT DT DC DT DC DA
HET ZN A 201 1
HET ZN A 202 1
HET ZN B 201 1
HET ZN B 202 1
HET ZN C 201 1
HET ZN C 202 1
HET ZN D 201 1
HET ZN D 202 1
HETNAM ZN ZINC ION
FORMUL 7 ZN 8(ZN 2+)
HELIX 1 1 THR A 4 ARG A 20 1 17
HELIX 2 2 THR A 25 GLN A 38 1 14
HELIX 3 3 SER A 43 GLU A 55 1 13
HELIX 4 4 LYS A 59 GLN A 73 1 15
HELIX 5 5 ALA A 114 MET A 128 1 15
HELIX 6 6 CYS A 143 CYS A 152 1 10
HELIX 7 7 THR B 4 ARG B 20 1 17
HELIX 8 8 THR B 25 GLN B 38 1 14
HELIX 9 9 SER B 43 GLU B 55 1 13
HELIX 10 10 LYS B 59 GLN B 73 1 15
HELIX 11 11 ALA B 114 MET B 128 1 15
HELIX 12 12 CYS B 143 CYS B 152 1 10
HELIX 13 13 THR C 6 ARG C 20 1 15
HELIX 14 14 THR C 25 GLN C 38 1 14
HELIX 15 15 SER C 43 GLU C 55 1 13
HELIX 16 16 LYS C 59 GLN C 73 1 15
HELIX 17 17 GLU C 80 ASN C 83 5 4
HELIX 18 18 ALA C 114 MET C 128 1 15
HELIX 19 19 CYS C 143 CYS C 152 1 10
HELIX 20 20 THR D 5 ARG D 20 1 16
HELIX 21 21 THR D 25 LEU D 37 1 13
HELIX 22 22 SER D 43 GLU D 55 1 13
HELIX 23 23 LYS D 59 GLN D 73 1 15
HELIX 24 24 ALA D 114 MET D 128 1 15
HELIX 25 25 CYS D 143 ALA D 151 1 9
SHEET 1 A 2 VAL A 76 VAL A 79 0
SHEET 2 A 2 SER A 84 LEU A 87 -1 O SER A 84 N VAL A 79
SHEET 1 B 6 VAL A 109 GLU A 112 0
SHEET 2 B 6 ALA A 99 CYS A 103 -1 N ALA A 99 O GLU A 112
SHEET 3 B 6 ALA A 131 LEU A 142 1 O ALA A 139 N MET A 100
SHEET 4 B 6 ALA D 131 LEU D 142 -1 O HIS D 134 N HIS A 140
SHEET 5 B 6 ALA D 99 CYS D 103 1 N MET D 100 O ALA D 139
SHEET 6 B 6 VAL D 109 GLU D 112 -1 O GLU D 112 N ALA D 99
SHEET 1 C 2 VAL B 76 VAL B 79 0
SHEET 2 C 2 SER B 84 LEU B 87 -1 O SER B 84 N VAL B 79
SHEET 1 D 6 VAL B 109 CYS B 113 0
SHEET 2 D 6 SER B 98 CYS B 103 -1 N ALA B 99 O GLU B 112
SHEET 3 D 6 ALA B 131 LEU B 142 1 O ALA B 139 N MET B 100
SHEET 4 D 6 ALA C 131 LEU C 142 -1 O GLU C 138 N VAL B 136
SHEET 5 D 6 SER C 98 CYS C 103 1 N MET C 100 O ALA C 139
SHEET 6 D 6 VAL C 109 CYS C 113 -1 O LYS C 110 N PHE C 101
SHEET 1 E 2 VAL C 76 VAL C 79 0
SHEET 2 E 2 SER C 84 LEU C 87 -1 O SER C 84 N VAL C 79
SHEET 1 F 2 VAL D 76 VAL D 79 0
SHEET 2 F 2 SER D 84 LEU D 87 -1 O VAL D 86 N HIS D 77
LINK NE2 HIS A 77 ZN ZN A 202 1555 1555 2.07
LINK SG CYS A 88 ZN ZN A 202 1555 1555 2.32
LINK NE2 HIS A 96 ZN ZN A 202 1555 1555 2.09
LINK SG CYS A 103 ZN ZN A 201 1555 1555 2.31
LINK SG CYS A 106 ZN ZN A 201 1555 1555 2.35
LINK OE1 GLU A 111 ZN ZN A 202 1555 1555 1.99
LINK OE2 GLU A 111 ZN ZN A 202 1555 1555 2.63
LINK SG CYS A 143 ZN ZN A 201 1555 1555 2.33
LINK SG CYS A 146 ZN ZN A 201 1555 1555 2.31
LINK NE2 HIS B 77 ZN ZN B 201 1555 1555 2.08
LINK SG CYS B 88 ZN ZN B 201 1555 1555 2.31
LINK NE2 HIS B 96 ZN ZN B 201 1555 1555 2.08
LINK SG CYS B 103 ZN ZN B 202 1555 1555 2.35
LINK SG CYS B 106 ZN ZN B 202 1555 1555 2.34
LINK OE1 GLU B 111 ZN ZN B 201 1555 1555 1.99
LINK SG CYS B 143 ZN ZN B 202 1555 1555 2.33
LINK SG CYS B 146 ZN ZN B 202 1555 1555 2.31
LINK NE2 HIS C 77 ZN ZN C 202 1555 1555 2.08
LINK SG CYS C 88 ZN ZN C 202 1555 1555 2.33
LINK NE2 HIS C 96 ZN ZN C 202 1555 1555 2.08
LINK SG CYS C 103 ZN ZN C 201 1555 1555 2.34
LINK SG CYS C 106 ZN ZN C 201 1555 1555 2.30
LINK OE1 GLU C 111 ZN ZN C 202 1555 1555 1.99
LINK SG CYS C 143 ZN ZN C 201 1555 1555 2.33
LINK SG CYS C 146 ZN ZN C 201 1555 1555 2.31
LINK NE2 HIS D 77 ZN ZN D 202 1555 1555 2.08
LINK SG CYS D 88 ZN ZN D 202 1555 1555 2.31
LINK NE2 HIS D 96 ZN ZN D 202 1555 1555 2.08
LINK SG CYS D 103 ZN ZN D 201 1555 1555 2.34
LINK SG CYS D 106 ZN ZN D 201 1555 1555 2.34
LINK OE1 GLU D 111 ZN ZN D 202 1555 1555 1.98
LINK OE2 GLU D 111 ZN ZN D 202 1555 1555 2.64
LINK SG CYS D 143 ZN ZN D 201 1555 1555 2.34
LINK SG CYS D 146 ZN ZN D 201 1555 1555 2.34
SITE 1 AC1 4 CYS A 103 CYS A 106 CYS A 143 CYS A 146
SITE 1 AC2 4 HIS A 77 CYS A 88 HIS A 96 GLU A 111
SITE 1 AC3 4 HIS B 77 CYS B 88 HIS B 96 GLU B 111
SITE 1 AC4 4 CYS B 103 CYS B 106 CYS B 143 CYS B 146
SITE 1 AC5 4 CYS C 103 CYS C 106 CYS C 143 CYS C 146
SITE 1 AC6 4 HIS C 77 CYS C 88 HIS C 96 GLU C 111
SITE 1 AC7 4 CYS D 103 CYS D 106 CYS D 143 CYS D 146
SITE 1 AC8 4 HIS D 77 CYS D 88 HIS D 96 GLU D 111
CRYST1 193.324 80.470 98.770 90.00 120.15 90.00 C 1 2 1 16
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 0.005173 0.000000 0.003005 0.00000
SCALE2 0.000000 0.012427 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011709 0.00000
(ATOM LINES ARE NOT SHOWN.)
END