HEADER DNA BINDING PROTEIN 22-MAY-26 27AE TITLE CRYSTAL STRUCTURE OF PROTEIN PF1862 FROM PYROCOCCUS FURIOSUS TITLE 2 CRYSTALLIZED AT 21 DEGREE CELSIUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS DSM 3638; SOURCE 3 ORGANISM_TAXID: 186497; SOURCE 4 STRAIN: DSM 3638; SOURCE 5 ATCC: 43587; SOURCE 6 GENE: PF1862; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: PLYSS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PET3A BASED; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PST50TRC2STRHISN KEYWDS DNA BINDING PROTEIN, NUCLEIC ACID-BINDING PROTEIN, PROTEIN OF UNKNOWN KEYWDS 2 FUNCTION (DUF655) EXPDTA X-RAY DIFFRACTION AUTHOR S.SHUBHANGI,S.S.GAIKWAD,S.S.TANEJA,S.BAIG,K.PALASIYAWALA,A.KUMAR, AUTHOR 2 R.D.MAKDE REVDAT 1 03-JUN-26 27AE 0 JRNL AUTH S.SHUBHANGI,S.S.GAIKWAD,S.S.TANEJA,S.BAIG,K.PALASIYAWALA, JRNL AUTH 2 A.KUMAR,R.D.MAKDE JRNL TITL CRYSTAL STRUCTURE OF PF1862 PROTEIN FROM PYROCOCCUS FURIOSUS JRNL TITL 2 CRYSTALLIZED AT 21 DEGREE CELSIUS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.LIEBSCHNER,P.V.AFONINE,M.L.BAKER,G.BUNKOCZI,V.B.CHEN, REMARK 1 AUTH 2 T.I.CROLL,B.HINTZE,L.W.HUNG,S.JAIN,A.J.MCCOY,N.W.MORIARTY, REMARK 1 AUTH 3 R.D.OEFFNER,B.K.POON,M.G.PRISANT,R.J.READ,J.S.RICHARDSON, REMARK 1 AUTH 4 D.C.RICHARDSON,M.D.SAMMITO,O.V.SOBOLEV,D.H.STOCKWELL, REMARK 1 AUTH 5 T.C.TERWILLIGER,A.G.URZHUMTSEV,L.L.VIDEAU,C.J.WILLIAMS, REMARK 1 AUTH 6 P.D.ADAMS REMARK 1 TITL MACROMOLECULAR STRUCTURE DETERMINATION USING X-RAYS, REMARK 1 TITL 2 NEUTRONS AND ELECTRONS: RECENT DEVELOPMENTS IN PHENIX REMARK 1 REF ACTA CRYSTALLOGR.SECT.D 2019 REMARK 1 REFN ESSN 1399-0047 REMARK 1 PMID 31588918 REMARK 1 DOI 10.1107/S2059798319011471 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 16930 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 823 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 37.7800 - 3.4500 1.00 2705 186 0.1479 0.1835 REMARK 3 2 3.4500 - 2.7400 1.00 2711 132 0.2061 0.2662 REMARK 3 3 2.7400 - 2.3900 1.00 2666 135 0.2207 0.2847 REMARK 3 4 2.3900 - 2.1700 1.00 2701 109 0.2170 0.2842 REMARK 3 5 2.1700 - 2.0200 1.00 2679 121 0.2369 0.2902 REMARK 3 6 2.0200 - 1.9000 0.99 2645 140 0.2599 0.3316 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) : 0.282 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.218 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.04 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 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 : 0.003 1541 REMARK 3 ANGLE : 0.558 2079 REMARK 3 CHIRALITY : 0.042 225 REMARK 3 PLANARITY : 0.004 266 REMARK 3 DIHEDRAL : 15.819 622 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 9.8518 0.1796 19.3442 REMARK 3 T TENSOR REMARK 3 T11: 0.2743 T22: 0.2464 REMARK 3 T33: 0.2067 T12: 0.0487 REMARK 3 T13: -0.0459 T23: 0.0090 REMARK 3 L TENSOR REMARK 3 L11: 3.9219 L22: 4.1705 REMARK 3 L33: 2.7750 L12: 0.5685 REMARK 3 L13: -1.7146 L23: -1.3965 REMARK 3 S TENSOR REMARK 3 S11: 0.1915 S12: 0.4816 S13: 0.1733 REMARK 3 S21: -0.2388 S22: 0.0536 S23: 0.2217 REMARK 3 S31: -0.0993 S32: -0.1404 S33: -0.2106 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 27AE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-MAY-26. REMARK 100 THE DEPOSITION ID IS D_1300074627. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-FEB-26 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : RRCAT INDUS-2 REMARK 200 BEAMLINE : PX-BL21 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.997 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16953 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 42.120 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.7000 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) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.89600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: ALPHAFOLD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS (PH 5.5) AND 17% PEG REMARK 280 10000; PROTEIN PF1862 AT 40 MG/ML, MICROBATCH, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 21.06000 REMARK 290 SMTRY3 2 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: 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: 9590 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 ASP A 37 REMARK 465 LEU A 38 REMARK 465 ARG A 39 REMARK 465 THR A 40 REMARK 465 GLY A 41 REMARK 465 HIS A 42 REMARK 465 TYR A 43 REMARK 465 LEU A 44 REMARK 465 GLY A 45 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 71 -3.77 75.75 REMARK 500 ILE A 129 -65.44 -105.21 REMARK 500 LYS A 157 130.37 -170.93 REMARK 500 REMARK 500 REMARK: NULL DBREF 27AE A 19 205 UNP Q8TZW3 Q8TZW3_PYRFU 19 205 SEQRES 1 A 187 VAL GLU TYR GLU GLU TYR ALA TYR VAL LEU ASP TYR LEU SEQRES 2 A 187 PRO ASN GLY TYR PRO ASP LEU ARG THR GLY HIS TYR LEU SEQRES 3 A 187 GLY LYS PRO VAL ALA GLN VAL ILE GLY GLU LYS ALA PHE SEQRES 4 A 187 THR LEU LEU GLU VAL THR PRO LYS VAL ASP LEU MET LEU SEQRES 5 A 187 TYR GLU ARG VAL TYR VAL GLY LYS GLY GLU ARG ASP LYS SEQRES 6 A 187 VAL LEU LYS ILE ASN LYS LYS LEU THR TYR ASP GLU LEU SEQRES 7 A 187 THR ASP THR ALA LYS ALA GLU LEU PRO TYR VAL LEU GLU SEQRES 8 A 187 GLU ILE VAL LYS ASN ASN GLU ASP ARG PHE VAL LYS PHE SEQRES 9 A 187 PHE ASN ILE ALA PRO PRO ILE THR ASN ARG LEU HIS SER SEQRES 10 A 187 LEU GLU LEU LEU PRO GLY ILE GLY LYS LYS HIS MET TRP SEQRES 11 A 187 GLU ILE ILE GLU GLU ARG GLU LYS LYS PRO PHE GLU SER SEQRES 12 A 187 PHE GLU ASP LEU LYS LYS ARG VAL LYS GLY LEU PRO ASP SEQRES 13 A 187 PRO VAL LYS MET ILE ALA LYS ARG ILE LEU GLU GLU LEU SEQRES 14 A 187 GLN GLY LYS ASP LYS TYR ARG LEU PHE VAL GLY SER ASN SEQRES 15 A 187 ARG ILE PHE ARG GLU FORMUL 2 HOH *163(H2 O) HELIX 1 AA1 THR A 92 LEU A 96 5 5 HELIX 2 AA2 THR A 97 ASN A 114 1 18 HELIX 3 AA3 ASN A 115 ALA A 126 1 12 HELIX 4 AA4 HIS A 134 LEU A 139 5 6 HELIX 5 AA5 GLY A 143 LYS A 157 1 15 HELIX 6 AA6 SER A 161 VAL A 169 1 9 HELIX 7 AA7 ASP A 174 GLN A 188 1 15 SHEET 1 AA1 5 ARG A 73 TYR A 75 0 SHEET 2 AA1 5 TYR A 24 LEU A 31 -1 N ALA A 25 O VAL A 74 SHEET 3 AA1 5 VAL A 48 GLY A 53 -1 O GLN A 50 N LEU A 28 SHEET 4 AA1 5 LEU A 59 PRO A 64 -1 O LEU A 60 N VAL A 51 SHEET 5 AA1 5 VAL A 84 LYS A 90 -1 O LYS A 89 N GLU A 61 CRYST1 39.768 42.120 66.807 90.00 106.26 90.00 P 1 21 1 2 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 0.025146 0.000000 0.007335 0.00000 SCALE2 0.000000 0.023742 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015592 0.00000 MASTER 254 0 0 7 5 0 0 6 1643 1 0 15 END