HEADER DNA BINDING PROTEIN 03-FEB-99 1B8Z
TITLE HU FROM THERMOTOGA MARITIMA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PROTEIN (HISTONELIKE PROTEIN HU);
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA;
SOURCE 3 ORGANISM_TAXID: 2336;
SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS THERMOTOGA MARITIMA, THERMOSTABLE DNA BINDING PROTEIN, DNA BINDING
KEYWDS 2 PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR E.CHRISTODOULOU,W.R.RYPNIEWSKI,C.E.VORGIAS
REVDAT 3 27-DEC-23 1B8Z 1 REMARK
REVDAT 2 24-FEB-09 1B8Z 1 VERSN
REVDAT 1 03-FEB-00 1B8Z 0
JRNL AUTH E.CHRISTODOULOU,C.E.VORGIAS
JRNL TITL CLONING, OVERPRODUCTION, PURIFICATION AND CRYSTALLIZATION OF
JRNL TITL 2 THE DNA BINDING PROTEIN HU FROM THE HYPERTHERMOPHILIC
JRNL TITL 3 EUBACTERIUM THERMOTOGA MARITIMA.
JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 54 1043 1998
JRNL REFN ISSN 0907-4449
JRNL PMID 9757133
JRNL DOI 10.1107/S0907444998000341
REMARK 2
REMARK 2 RESOLUTION. 1.60 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 21554
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) : NULL
REMARK 3 R VALUE (WORKING SET) : 0.215
REMARK 3 FREE R VALUE : 0.236
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1078
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1040
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 77
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 19.82
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.04
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): NULL
REMARK 3 ESU BASED ON FREE R VALUE (A): NULL
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA
REMARK 3 BOND LENGTH (A) : 0.010 ; 0.020
REMARK 3 ANGLE DISTANCE (A) : 0.022 ; 0.040
REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.025 ; 0.050
REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL
REMARK 3
REMARK 3 PLANE RESTRAINT (A) : 0.015 ; 0.030
REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.089 ; 0.030
REMARK 3
REMARK 3 NON-BONDED CONTACT RESTRAINTS.
REMARK 3 SINGLE TORSION (A) : 0.177 ; 0.300
REMARK 3 MULTIPLE TORSION (A) : 0.269 ; 0.300
REMARK 3 H-BOND (X...Y) (A) : 0.137 ; 0.300
REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL
REMARK 3
REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS.
REMARK 3 SPECIFIED (DEGREES) : 20.000; NULL
REMARK 3 PLANAR (DEGREES) : 2.400 ; 25.000
REMARK 3 STAGGERED (DEGREES) : 13.200; 15.000
REMARK 3 TRANSVERSE (DEGREES) : 13.100; 20.000
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : 1.829 ; 3.000
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.696 ; 5.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 4.626 ; 6.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.954 ; 8.000
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1B8Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-FEB-99.
REMARK 100 THE DEPOSITION ID IS D_1000000445.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : 277
REMARK 200 PH : 4.6
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG
REMARK 200 BEAMLINE : BW7B
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.8833
REMARK 200 MONOCHROMATOR : SI(111)
REMARK 200 OPTICS : MIRROR
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21552
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 5.900
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 5.60000
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 59.0000
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 46.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.6
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43
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 -Y,X,Z+3/4
REMARK 290 4555 Y,-X,Z+1/4
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 38.78000
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 58.17000
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.39000
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: 3780 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 7770 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 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 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 ARG A 53
REMARK 465 LYS A 54
REMARK 465 ALA A 55
REMARK 465 ALA A 56
REMARK 465 ALA A 57
REMARK 465 ARG A 58
REMARK 465 LYS A 59
REMARK 465 GLY A 60
REMARK 465 VAL A 61
REMARK 465 ASN A 62
REMARK 465 PRO A 63
REMARK 465 GLN A 64
REMARK 465 THR A 65
REMARK 465 ARG A 66
REMARK 465 LYS A 67
REMARK 465 PRO A 68
REMARK 465 ILE A 69
REMARK 465 THR A 70
REMARK 465 ILE A 71
REMARK 465 PRO A 72
REMARK 465 GLU A 73
REMARK 465 ARG A 74
REMARK 465 LYS A 75
REMARK 465 ARG B 53
REMARK 465 LYS B 54
REMARK 465 ALA B 55
REMARK 465 ALA B 56
REMARK 465 ALA B 57
REMARK 465 ARG B 58
REMARK 465 LYS B 59
REMARK 465 GLY B 60
REMARK 465 VAL B 61
REMARK 465 ASN B 62
REMARK 465 PRO B 63
REMARK 465 GLN B 64
REMARK 465 THR B 65
REMARK 465 ARG B 66
REMARK 465 LYS B 67
REMARK 465 PRO B 68
REMARK 465 ILE B 69
REMARK 465 THR B 70
REMARK 465 ILE B 71
REMARK 465 PRO B 72
REMARK 465 GLU B 73
REMARK 465 ARG B 74
REMARK 465 LYS B 75
REMARK 480
REMARK 480 ZERO OCCUPANCY ATOM
REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO
REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS
REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 480 M RES C SSEQI ATOMS
REMARK 480 LYS A 4 CD CE NZ
REMARK 480 LYS A 17 NZ
REMARK 480 LYS A 22 CD CE NZ
REMARK 480 GLU A 30 CG CD OE1 OE2
REMARK 480 LYS A 41 CE NZ
REMARK 480 LYS A 78 CG CD CE NZ
REMARK 480 LYS A 80 CG CD CE NZ
REMARK 480 LYS A 83 CA CB CG CD CE NZ
REMARK 480 GLU A 87 CG CD OE1 OE2
REMARK 480 LYS A 90 CB CG CD CE NZ
REMARK 480 LYS B 78 CG CD CE NZ
REMARK 480 LYS B 80 CG CD CE NZ
REMARK 480 LYS B 83 CG CD CE NZ
REMARK 480 LYS B 86 CG CD CE NZ
REMARK 480 GLU B 87 CG CD OE1 OE2
REMARK 480 LYS B 88 CG CD CE NZ
REMARK 480 LYS B 90 CB CG CD CE NZ
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 PHE A 47 -65.35 -136.32
REMARK 500 PHE B 47 -62.72 -140.37
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1B8Z A 1 90 UNP P36206 DBH_THEMA 1 90
DBREF 1B8Z B 1 90 UNP P36206 DBH_THEMA 1 90
SEQRES 1 A 90 MET ASN LYS LYS GLU LEU ILE ASP ARG VAL ALA LYS LYS
SEQRES 2 A 90 ALA GLY ALA LYS LYS LYS ASP VAL LYS LEU ILE LEU ASP
SEQRES 3 A 90 THR ILE LEU GLU THR ILE THR GLU ALA LEU ALA LYS GLY
SEQRES 4 A 90 GLU LYS VAL GLN ILE VAL GLY PHE GLY SER PHE GLU VAL
SEQRES 5 A 90 ARG LYS ALA ALA ALA ARG LYS GLY VAL ASN PRO GLN THR
SEQRES 6 A 90 ARG LYS PRO ILE THR ILE PRO GLU ARG LYS VAL PRO LYS
SEQRES 7 A 90 PHE LYS PRO GLY LYS ALA LEU LYS GLU LYS VAL LYS
SEQRES 1 B 90 MET ASN LYS LYS GLU LEU ILE ASP ARG VAL ALA LYS LYS
SEQRES 2 B 90 ALA GLY ALA LYS LYS LYS ASP VAL LYS LEU ILE LEU ASP
SEQRES 3 B 90 THR ILE LEU GLU THR ILE THR GLU ALA LEU ALA LYS GLY
SEQRES 4 B 90 GLU LYS VAL GLN ILE VAL GLY PHE GLY SER PHE GLU VAL
SEQRES 5 B 90 ARG LYS ALA ALA ALA ARG LYS GLY VAL ASN PRO GLN THR
SEQRES 6 B 90 ARG LYS PRO ILE THR ILE PRO GLU ARG LYS VAL PRO LYS
SEQRES 7 B 90 PHE LYS PRO GLY LYS ALA LEU LYS GLU LYS VAL LYS
FORMUL 3 HOH *77(H2 O)
HELIX 1 1 LYS A 3 ALA A 14 1 12
HELIX 2 2 LYS A 18 LYS A 38 1 21
HELIX 3 3 LYS A 83 LYS A 88 1 6
HELIX 4 4 LYS B 3 ALA B 14 1 12
HELIX 5 5 LYS B 18 ALA B 37 1 20
HELIX 6 6 LYS B 83 LYS B 88 1 6
SHEET 1 A 3 VAL A 42 ILE A 44 0
SHEET 2 A 3 GLY A 48 GLU A 51 -1 N PHE A 50 O VAL A 42
SHEET 3 A 3 LYS A 78 PRO A 81 -1 N LYS A 80 O SER A 49
SHEET 1 B 3 VAL B 42 ILE B 44 0
SHEET 2 B 3 GLY B 48 GLU B 51 -1 N PHE B 50 O VAL B 42
SHEET 3 B 3 LYS B 78 PRO B 81 -1 N LYS B 80 O SER B 49
CRYST1 46.120 46.120 77.560 90.00 90.00 90.00 P 43 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 0.021682 0.000000 0.000000 0.00000
SCALE2 0.000000 0.021682 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012893 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
