HEADER DNA BINDING PROTEIN 19-JUL-23 8PW2 TITLE PROTEIN P6 FROM BACTERIOPHAGE PHI29, C-TERMINAL DELTA31 TRUNCATED TITLE 2 VERSION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LIKE PROTEIN P6; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DOUBLE-STRANDED DNA-BINDING PROTEIN P6,GENE PRODUCT 6,GP6, COMPND 5 NUCLEOID-ASSOCIATED PROTEIN P6,PROTEIN P6; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALASVIRUS PHI29; SOURCE 3 ORGANISM_TAXID: 10756; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HISTONE-LIKE, BACILLUS SUBTILLIS PHAGE, PHI29, NUCLEOCOMPLEX, P6, DNA KEYWDS 2 SUPERHELIX, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.ALCORLO PAGES,J.HERMOSO DOMINGUEZ REVDAT 3 06-MAR-24 8PW2 1 JRNL REVDAT 2 07-FEB-24 8PW2 1 JRNL REVDAT 1 17-JAN-24 8PW2 0 JRNL AUTH M.ALCORLO,J.R.LUQUE-ORTEGA,F.GAGO,A.ORTEGA,M.CASTELLANOS, JRNL AUTH 2 P.CHACON,M.DE VEGA,L.BLANCO,J.M.HERMOSO,M.SERRANO,G.RIVAS, JRNL AUTH 3 J.A.HERMOSO JRNL TITL FLEXIBLE STRUCTURAL ARRANGEMENT AND DNA-BINDING PROPERTIES JRNL TITL 2 OF PROTEIN P6 FROM BACILLUS SUBTILLIS PHAGE PHI 29. JRNL REF NUCLEIC ACIDS RES. V. 52 2045 2024 JRNL REFN ESSN 1362-4962 JRNL PMID 38281216 JRNL DOI 10.1093/NAR/GKAE041 REMARK 2 REMARK 2 RESOLUTION. 1.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20_4459 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) : 1.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 11555 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 569 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 32.3500 - 2.5200 1.00 2865 150 0.1941 0.1906 REMARK 3 2 2.5200 - 2.0000 0.99 2758 115 0.2497 0.2582 REMARK 3 3 2.0000 - 1.7500 0.99 2706 153 0.2302 0.2811 REMARK 3 4 1.7500 - 1.5900 0.98 2657 151 0.2903 0.3171 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.607 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.79 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.59 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 : 0.009 508 REMARK 3 ANGLE : 1.076 697 REMARK 3 CHIRALITY : 0.066 85 REMARK 3 PLANARITY : 0.010 90 REMARK 3 DIHEDRAL : 4.961 71 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 8 THROUGH 29 ) REMARK 3 ORIGIN FOR THE GROUP (A): 35.1349 -5.3787 -2.2126 REMARK 3 T TENSOR REMARK 3 T11: 0.2816 T22: 0.2545 REMARK 3 T33: 0.2756 T12: 0.0068 REMARK 3 T13: 0.0041 T23: -0.0411 REMARK 3 L TENSOR REMARK 3 L11: 2.6076 L22: 4.6328 REMARK 3 L33: 1.0345 L12: 1.7683 REMARK 3 L13: -0.1479 L23: 0.4389 REMARK 3 S TENSOR REMARK 3 S11: 0.0506 S12: 0.0697 S13: 0.2017 REMARK 3 S21: 0.2585 S22: 0.1750 S23: -0.4543 REMARK 3 S31: -0.1834 S32: 0.0838 S33: -0.1722 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 30 THROUGH 51 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.5071 -11.8442 -1.7775 REMARK 3 T TENSOR REMARK 3 T11: 0.2596 T22: 0.2508 REMARK 3 T33: 0.2774 T12: 0.0316 REMARK 3 T13: 0.0113 T23: 0.0236 REMARK 3 L TENSOR REMARK 3 L11: 4.0475 L22: 4.9012 REMARK 3 L33: 3.2437 L12: 2.3000 REMARK 3 L13: -0.5939 L23: -0.4088 REMARK 3 S TENSOR REMARK 3 S11: -0.0211 S12: 0.1666 S13: 0.5965 REMARK 3 S21: 0.2599 S22: 0.1130 S23: 0.5319 REMARK 3 S31: -0.2997 S32: -0.2276 S33: -0.0840 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 52 THROUGH 67 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.5407 -11.1733 -3.5947 REMARK 3 T TENSOR REMARK 3 T11: 0.3202 T22: 0.2972 REMARK 3 T33: 0.2134 T12: -0.0164 REMARK 3 T13: 0.0172 T23: -0.0065 REMARK 3 L TENSOR REMARK 3 L11: 5.8134 L22: 0.9544 REMARK 3 L33: 3.0711 L12: 1.6558 REMARK 3 L13: -0.8101 L23: -1.4045 REMARK 3 S TENSOR REMARK 3 S11: -0.1141 S12: -0.0619 S13: 0.0496 REMARK 3 S21: 0.5911 S22: 0.0349 S23: 0.2435 REMARK 3 S31: -0.0553 S32: 0.1015 S33: -0.2037 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 8PW2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1292132056. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUN-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11565 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.590 REMARK 200 RESOLUTION RANGE LOW (A) : 41.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 19.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 37.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.02600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM BIS TRIS PROPANE PH 7.0 AND 1.3 REMARK 280 M DI-AMMONIUM TARTRATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 13.88933 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.77867 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.77867 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 13.88933 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 ALA A 1 REMARK 465 LYS A 2 REMARK 465 MET A 3 REMARK 465 MET A 4 REMARK 465 GLN A 5 REMARK 465 ARG A 6 REMARK 465 GLU A 7 REMARK 465 VAL A 68 REMARK 465 TYR A 69 REMARK 465 GLU A 70 REMARK 465 LEU A 71 REMARK 465 PRO A 72 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 TYR A 52 66.21 -101.01 REMARK 500 REMARK 500 REMARK: NULL DBREF 8PW2 A 1 72 UNP P03685 NP_BPPH2 2 73 SEQRES 1 A 72 ALA LYS MET MET GLN ARG GLU ILE THR LYS THR THR VAL SEQRES 2 A 72 ASN VAL ALA LYS MET VAL MET VAL ASP GLY GLU VAL GLN SEQRES 3 A 72 VAL GLU GLN LEU PRO SER GLU THR PHE VAL GLY ASN LEU SEQRES 4 A 72 THR MET GLU GLN ALA GLN TRP ARG MET LYS ARG LYS TYR SEQRES 5 A 72 LYS GLY GLU PRO VAL GLN VAL VAL SER VAL GLU PRO ASN SEQRES 6 A 72 THR GLU VAL TYR GLU LEU PRO FORMUL 2 HOH *27(H2 O) HELIX 1 AA1 THR A 40 TYR A 52 1 13 SHEET 1 AA1 3 GLU A 24 GLN A 29 0 SHEET 2 AA1 3 LYS A 10 VAL A 21 -1 N VAL A 21 O GLU A 24 SHEET 3 AA1 3 GLU A 33 VAL A 36 -1 O GLU A 33 N VAL A 13 SHEET 1 AA2 3 GLU A 24 GLN A 29 0 SHEET 2 AA2 3 LYS A 10 VAL A 21 -1 N VAL A 21 O GLU A 24 SHEET 3 AA2 3 VAL A 57 ASN A 65 -1 O VAL A 60 N ASN A 14 CRYST1 59.257 59.257 41.668 90.00 90.00 120.00 P 31 2 1 6 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 0.016876 0.009743 0.000000 0.00000 SCALE2 0.000000 0.019486 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023999 0.00000