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 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 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