HEADER DNA BINDING PROTEIN 19-JAN-99 1B67 TITLE CRYSTAL STRUCTURE OF THE HISTONE HMFA FROM METHANOTHERMUS FERVIDUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (HISTONE HMFA); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOTHERMUS FERVIDUS; SOURCE 3 ORGANISM_TAXID: 2180; SOURCE 4 GENE: HMFA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: JM105; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PKS354 KEYWDS HISTONE, HMF1, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.DECANNIERE,K.SANDMAN,J.N.REEVE,U.HEINEMANN REVDAT 5 03-APR-24 1B67 1 REMARK REVDAT 4 27-DEC-23 1B67 1 REMARK REVDAT 3 24-FEB-09 1B67 1 VERSN REVDAT 2 18-OCT-00 1B67 1 JRNL REVDAT 1 17-JAN-00 1B67 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 HYPERTHERMOPHYLE, 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. 1.48 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 11.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.193 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.188 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1044 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 20400 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 986 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 77 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 ANGLE DISTANCES (A) : 0.028 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.054 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT AGAINST I'S REMARK 4 REMARK 4 1B67 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-AUG-99. REMARK 100 THE DEPOSITION ID IS D_1000007236. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-95 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 6.5 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 : X31 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : CCP4 (AGROVATA, SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 77006 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480 REMARK 200 RESOLUTION RANGE LOW (A) : 11.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 5.70000 REMARK 200 FOR THE DATA SET : 2.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 25.6000 REMARK 200 FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE (CCP4), CCP4 REMARK 200 STARTING MODEL: NMR MODEL OF HMFB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLISATION IN HANGING DROP REMARK 280 RESERVOIR: 2.6 M (NH4)2SO4 PROTEIN WAS MIXED 1 TO 1 WITH REMARK 280 RESERVOIR SOLUTION, PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 16.86000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.75000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.29000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.75000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.86000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.29000 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 REMARK 350 TOTAL BURIED SURFACE AREA: 3420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 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 GLY B 102 REMARK 465 PHE B 168 REMARK 465 LYS B 169 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 ASP A 23 CG OD1 OD2 REMARK 470 ASP A 24 CG OD1 OD2 REMARK 470 LYS A 31 CE NZ REMARK 470 LYS A 46 CD CE NZ REMARK 470 LYS A 49 CG CD CE NZ REMARK 470 LYS A 57 CD CE NZ REMARK 470 LYS B 157 CD CE NZ 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 ARG A 65 NE - CZ - NH1 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG B 126 NE - CZ - NH1 ANGL. DEV. = -3.0 DEGREES REMARK 500 GLU B 162 CB - CG - CD ANGL. DEV. = 21.2 DEGREES REMARK 500 GLU B 162 OE1 - CD - OE2 ANGL. DEV. = -8.5 DEGREES 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 LEU B 104 116.77 29.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 301 DBREF 1B67 A 2 69 UNP P48781 HMFA_METFE 2 69 DBREF 1B67 B 102 169 UNP P48781 HMFA_METFE 2 69 SEQRES 1 A 68 GLY GLU LEU PRO ILE ALA PRO ILE GLY ARG ILE ILE LYS SEQRES 2 A 68 ASN ALA GLY ALA GLU ARG VAL SER ASP ASP ALA ARG ILE SEQRES 3 A 68 ALA LEU ALA LYS VAL LEU GLU GLU MET GLY GLU GLU ILE SEQRES 4 A 68 ALA SER GLU ALA VAL LYS LEU ALA LYS HIS ALA GLY ARG SEQRES 5 A 68 LYS THR ILE LYS ALA GLU ASP ILE GLU LEU ALA ARG LYS SEQRES 6 A 68 MET PHE LYS SEQRES 1 B 68 GLY GLU LEU PRO ILE ALA PRO ILE GLY ARG ILE ILE LYS SEQRES 2 B 68 ASN ALA GLY ALA GLU ARG VAL SER ASP ASP ALA ARG ILE SEQRES 3 B 68 ALA LEU ALA LYS VAL LEU GLU GLU MET GLY GLU GLU ILE SEQRES 4 B 68 ALA SER GLU ALA VAL LYS LEU ALA LYS HIS ALA GLY ARG SEQRES 5 B 68 LYS THR ILE LYS ALA GLU ASP ILE GLU LEU ALA ARG LYS SEQRES 6 B 68 MET PHE LYS HET SO4 A 301 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *77(H2 O) HELIX 1 1 ILE A 6 ASN A 15 1 10 HELIX 2 2 ASP A 23 HIS A 50 1 28 HELIX 3 3 ALA A 58 MET A 67 1 10 HELIX 4 4 ILE B 106 ASN B 115 1 10 HELIX 5 5 ASP B 123 ALA B 151 1 29 HELIX 6 6 ALA B 158 ARG B 165 1 8 SHEET 1 A 2 ARG A 20 VAL A 21 0 SHEET 2 A 2 THR B 155 ILE B 156 1 N ILE B 156 O VAL A 21 SHEET 1 B 2 THR A 55 ILE A 56 0 SHEET 2 B 2 ARG B 120 VAL B 121 1 O ARG B 120 N LYS A 57 SITE 1 AC1 5 ARG A 20 ARG A 53 LYS A 54 THR A 55 SITE 2 AC1 5 ARG B 120 CRYST1 33.720 52.580 67.500 90.00 90.00 90.00 P 21 21 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 0.029656 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019019 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014815 0.00000 MTRIX1 1 -0.090630 0.245700 0.965100 -17.34369 1 MTRIX2 1 0.273520 -0.925680 0.261350 28.27693 1 MTRIX3 1 0.957590 0.287650 0.016690 8.62265 1