HEADER HISTONE 18-MAR-98 1A7W TITLE CRYSTAL STRUCTURE OF THE HISTONE HMFB FROM METHANOTHERMUS FERVIDUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE HMFB; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOTHERMUS FERVIDUS; SOURCE 3 ORGANISM_TAXID: 2180; SOURCE 4 GENE: HMFB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_GENE: HMFB KEYWDS HISTONE EXPDTA X-RAY DIFFRACTION AUTHOR K.DECANNIERE,K.SANDMAN,J.N.REEVE,U.HEINEMANN REVDAT 5 03-APR-24 1A7W 1 REMARK REVDAT 4 07-FEB-24 1A7W 1 REMARK LINK REVDAT 3 13-JUL-11 1A7W 1 VERSN REVDAT 2 24-FEB-09 1A7W 1 VERSN REVDAT 1 23-MAR-99 1A7W 0 JRNL AUTH K.DECANNIERE,A.M.BABU,K.SANDMAN,J.N.REEVE,U.HEINEMANN JRNL TITL CRYSTAL STRUCTURES OF RECOMBINANT HISTONES HMFA AND HMFB JRNL TITL 2 FROM THE HYPERTHERMOPHILIC ARCHAEON METHANOTHERMUS FERVIDUS. JRNL REF J.MOL.BIOL. V. 303 35 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 11021968 JRNL DOI 10.1006/JMBI.2000.4104 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.DECANNIERE,K.SANDMAN,J.N.REEVE,U.HEINEMANN REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY CHARACTERIZATION OF REMARK 1 TITL 2 THE METHANOTHERMUS FERVIDUS HISTONES HMFA AND HMFB REMARK 1 REF PROTEINS V. 24 269 1996 REMARK 1 REFN ISSN 0887-3585 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.R.STARICH,K.SANDMAN,J.N.REEVE,M.F.SUMMERS REMARK 1 TITL NMR STRUCTURE OF HMFB FROM THE HYPERTHERMOPHILE, REMARK 1 TITL 2 METHANOTHERMUS FERVIDUS, CONFIRMS THAT THIS ARCHAEAL PROTEIN REMARK 1 TITL 3 IS A HISTONE REMARK 1 REF J.MOL.BIOL. V. 255 187 1996 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 1.55 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 10797 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : AFTER RIGID BODY REFINEMENT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 520 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 527 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 46 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.87 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.39800 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 1.39800 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : -2.69000 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) : 0.022 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.039 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.047 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.024 ; 0.030 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.161 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.178 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.300 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.300 ; NULL REMARK 3 H-BOND (X-H...Y) (A) : 0.300 ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : 0.000 ; 15.000 REMARK 3 PLANAR (DEGREES) : 3.900 ; 7.000 REMARK 3 STAGGERED (DEGREES) : 17.700; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 4.500 ; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.932 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.676 ; 3.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.426 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.241 ; 3.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RIGID BODY WITH AMORE, SIMULATED REMARK 3 ANNEALING WITH X-PLOR, REFINEMENT WITH REFMAC. ESD FROM LUZZATI REMARK 3 PLOT (A) : 0.25 REMARK 4 REMARK 4 1A7W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170503. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : FEB-95 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL 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 RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FOIL REMARK 200 OPTICS : SUPPER NI-COATED MIRROR SYSTEM REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : CCP4 (AGROVATA, SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6152 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 39.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : 0.05300 REMARK 200 FOR THE DATA SET : 8.3000 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) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.19600 REMARK 200 R SYM FOR SHELL (I) : 0.19600 REMARK 200 FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PARTIALLY REFINED ORTHORHOMBIC HMFA REMARK 200 REMARK 200 REMARK: ORTHOROMBIC HMFA STRUCTURE WILL BE SUBMITTED SOON REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 15.65000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.79000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.65000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.79000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 3620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -95.0 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 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 LYS A 69 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 ASP A 23 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ASP A 38 CB - CG - OD2 ANGL. DEV. = -8.0 DEGREES REMARK 500 ARG A 48 CD - NE - CZ ANGL. DEV. = 9.7 DEGREES REMARK 500 ARG A 66 CD - NE - CZ ANGL. DEV. = 12.1 DEGREES 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 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 34 OE2 REMARK 620 2 ASP A 38 OD2 112.7 REMARK 620 3 HIS A 49 ND1 91.4 128.9 REMARK 620 N 1 2 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 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 102 DBREF 1A7W A 1 69 UNP P19267 HMFB_METFE 1 69 SEQRES 1 A 69 MET GLU LEU PRO ILE ALA PRO ILE GLY ARG ILE ILE LYS SEQRES 2 A 69 ASP ALA GLY ALA GLU ARG VAL SER ASP ASP ALA ARG ILE SEQRES 3 A 69 THR LEU ALA LYS ILE LEU GLU GLU MET GLY ARG ASP ILE SEQRES 4 A 69 ALA SER GLU ALA ILE LYS LEU ALA ARG HIS ALA GLY ARG SEQRES 5 A 69 LYS THR ILE LYS ALA GLU ASP ILE GLU LEU ALA VAL ARG SEQRES 6 A 69 ARG PHE LYS LYS HET ZN A 101 1 HET CL A 102 1 HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION FORMUL 2 ZN ZN 2+ FORMUL 3 CL CL 1- FORMUL 4 HOH *46(H2 O) HELIX 1 1 ILE A 5 ASP A 14 1 10 HELIX 2 2 ASP A 22 ALA A 50 1 29 HELIX 3 3 ALA A 57 ARG A 66 1 10 LINK OE2 GLU A 34 ZN ZN A 101 1555 1555 2.02 LINK OD2 ASP A 38 ZN ZN A 101 1555 1555 2.02 LINK ND1 HIS A 49 ZN ZN A 101 4456 1555 2.10 SITE 1 AC1 4 GLU A 34 ASP A 38 HIS A 49 CL A 102 SITE 1 AC2 3 ASP A 38 ZN A 101 HOH A 155 CRYST1 31.300 61.580 39.650 90.00 90.00 90.00 P 21 21 2 4 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 0.031949 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016239 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025221 0.00000