HEADER DNA BINDING PROTEIN 19-JAN-23 8FVX TITLE HISTONE FROM BDELLOVIBRIO BACTERIOVORUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CBFD_NFYB_HMF DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BDELLOVIBRIO BACTERIOVORUS HD100; SOURCE 3 ORGANISM_TAXID: 264462; SOURCE 4 GENE: BD0055; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HISTONE, NAP, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.P.LAURSEN,K.LUGER REVDAT 2 13-MAR-24 8FVX 1 JRNL REVDAT 1 30-AUG-23 8FVX 0 JRNL AUTH A.HOCHER,S.P.LAURSEN,P.RADFORD,J.TYSON,C.LAMBERT, JRNL AUTH 2 K.M.STEVENS,A.MONTOYA,P.V.SHLIAHA,M.PICARDEAU,R.E.SOCKETT, JRNL AUTH 3 K.LUGER,T.WARNECKE JRNL TITL HISTONES WITH AN UNCONVENTIONAL DNA-BINDING MODE IN VITRO JRNL TITL 2 ARE MAJOR CHROMATIN CONSTITUENTS IN THE BACTERIUM JRNL TITL 3 BDELLOVIBRIO BACTERIOVORUS. JRNL REF NAT MICROBIOL V. 8 2006 2023 JRNL REFN ESSN 2058-5276 JRNL PMID 37814071 JRNL DOI 10.1038/S41564-023-01492-X REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 5156 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 461 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.3900 - 2.8600 1.00 1233 137 0.1832 0.2106 REMARK 3 2 2.8600 - 2.2700 1.00 1160 129 0.2016 0.2673 REMARK 3 3 2.2700 - 1.9800 1.00 1140 127 0.1752 0.2360 REMARK 3 4 1.9800 - 1.8000 0.98 1107 123 0.1952 0.2428 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.145 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.564 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.63 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.61 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 476 REMARK 3 ANGLE : 0.816 636 REMARK 3 CHIRALITY : 0.053 83 REMARK 3 PLANARITY : 0.005 77 REMARK 3 DIHEDRAL : 4.940 64 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8FVX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1000271416. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-OCT-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-003 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.541870 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5959 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.670 REMARK 200 RESOLUTION RANGE LOW (A) : 29.390 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.7 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.05163 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.10290 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 10.42 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: FLAT RHOMBOID REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.2 M (NH4)2SO4, 100 MM BICINE, PH 9, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.20600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.24200 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 17.20600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.24200 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: 3660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 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 34.41200 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 56.48400 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 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 GLU A 3 77.16 51.58 REMARK 500 HIS A 63 2.82 -68.35 REMARK 500 REMARK 500 REMARK: NULL DBREF 8FVX A 1 64 UNP Q6MRM1 Q6MRM1_BDEBA 1 64 SEQRES 1 A 64 MET ALA GLU VAL LEU VAL VAL THR SER LYS VAL LYS LYS SEQRES 2 A 64 LEU ILE LYS GLU LYS GLY GLN MET ASN THR SER ALA GLU SEQRES 3 A 64 THR ILE ASP VAL LEU SER LYS ALA ILE GLU GLN LEU CYS SEQRES 4 A 64 LEU LYS GLY VAL GLU SER ALA LYS ALA ASP GLY ARG LYS SEQRES 5 A 64 THR VAL MET ALA ARG ASP ILE VAL ILE ASP HIS LEU FORMUL 2 HOH *43(H2 O) HELIX 1 AA1 VAL A 7 GLN A 20 1 14 HELIX 2 AA2 SER A 24 ASP A 49 1 26 HELIX 3 AA3 MET A 55 ILE A 59 5 5 CRYST1 26.772 34.412 56.484 90.00 90.00 90.00 P 2 21 21 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 0.037352 0.000000 0.000000 0.00000 SCALE2 0.000000 0.029060 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017704 0.00000 TER 477 LEU A 64 HETATM 478 O HOH A 101 20.778 28.759 43.509 1.00 15.24 O HETATM 479 O HOH A 102 21.999 4.347 48.796 1.00 15.19 O HETATM 480 O HOH A 103 31.961 28.555 16.895 1.00 16.78 O HETATM 481 O HOH A 104 35.806 16.820 23.057 1.00 18.53 O HETATM 482 O HOH A 105 30.370 19.549 22.061 1.00 24.83 O HETATM 483 O HOH A 106 31.008 22.890 17.444 1.00 13.65 O HETATM 484 O HOH A 107 33.778 22.950 5.517 1.00 14.81 O HETATM 485 O HOH A 108 17.643 24.389 45.442 1.00 21.18 O HETATM 486 O HOH A 109 29.031 16.976 4.360 1.00 23.93 O HETATM 487 O HOH A 110 9.760 12.194 38.685 1.00 14.20 O HETATM 488 O HOH A 111 31.730 17.815 14.816 1.00 17.09 O HETATM 489 O HOH A 112 10.977 9.308 45.526 1.00 25.29 O HETATM 490 O HOH A 113 25.633 28.148 17.140 1.00 5.24 O HETATM 491 O HOH A 114 8.697 3.743 37.869 1.00 21.37 O HETATM 492 O HOH A 115 15.124 23.956 38.363 1.00 16.86 O HETATM 493 O HOH A 116 27.542 27.625 22.372 1.00 21.65 O HETATM 494 O HOH A 117 37.710 14.271 24.943 1.00 25.78 O HETATM 495 O HOH A 118 24.222 25.740 6.416 1.00 12.84 O HETATM 496 O HOH A 119 32.100 20.441 11.057 1.00 12.58 O HETATM 497 O HOH A 120 15.593 12.530 42.161 1.00 7.90 O HETATM 498 O HOH A 121 23.599 23.213 2.442 1.00 23.13 O HETATM 499 O HOH A 122 27.960 19.864 20.561 1.00 12.12 O HETATM 500 O HOH A 123 14.261 15.224 44.070 1.00 17.57 O HETATM 501 O HOH A 124 26.772 26.639 6.312 1.00 10.84 O HETATM 502 O HOH A 125 11.528 12.732 46.110 1.00 37.87 O HETATM 503 O HOH A 126 26.883 23.673 1.408 1.00 30.83 O HETATM 504 O HOH A 127 16.594 25.866 32.023 1.00 23.19 O HETATM 505 O HOH A 128 19.761 29.997 22.928 1.00 24.30 O HETATM 506 O HOH A 129 15.378 28.078 36.507 1.00 29.70 O HETATM 507 O HOH A 130 25.678 23.752 32.305 1.00 11.52 O HETATM 508 O HOH A 131 11.391 0.984 38.673 1.00 22.13 O HETATM 509 O HOH A 132 10.401 8.266 26.953 1.00 26.69 O HETATM 510 O HOH A 133 16.667 27.078 44.382 1.00 23.68 O HETATM 511 O HOH A 134 15.925 24.438 33.609 1.00 24.35 O HETATM 512 O HOH A 135 12.986 12.881 43.098 1.00 20.22 O HETATM 513 O HOH A 136 24.020 25.339 3.499 1.00 20.73 O HETATM 514 O HOH A 137 33.690 20.832 8.796 1.00 25.10 O HETATM 515 O HOH A 138 26.873 24.950 30.372 1.00 19.99 O HETATM 516 O HOH A 139 11.029 12.152 41.522 1.00 26.54 O HETATM 517 O HOH A 140 20.727 14.590 7.335 1.00 36.06 O HETATM 518 O HOH A 141 19.980 29.660 41.096 1.00 24.36 O HETATM 519 O HOH A 142 20.524 21.434 47.130 1.00 24.21 O HETATM 520 O HOH A 143 5.738 13.558 37.702 1.00 27.99 O MASTER 225 0 0 3 0 0 0 6 519 1 0 5 END