HEADER DNA BINDING PROTEIN 11-JAN-21 7DUT TITLE STRUCTURE OF SULFOLOBUS SOLFATARICUS SEGA PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SOJ PROTEIN (SOJ); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROLOBUS SOLFATARICUS (STRAIN ATCC 35092 / SOURCE 3 DSM 1617 / JCM 11322 / P2); SOURCE 4 ORGANISM_TAXID: 273057; SOURCE 5 STRAIN: ATCC 35092 / DSM 1617 / JCM 11322 / P2; SOURCE 6 GENE: SOJ, SSO0034; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PARTITION PROTEIN, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.Y.YEN,M.G.LIN,C.D.HSIAO,Y.J.SUN REVDAT 3 29-NOV-23 7DUT 1 REMARK REVDAT 2 16-FEB-22 7DUT 1 JRNL REVDAT 1 22-DEC-21 7DUT 0 JRNL AUTH C.Y.YEN,M.G.LIN,B.W.CHEN,I.W.NG,N.READ,A.F.KABLI,C.T.WU, JRNL AUTH 2 Y.Y.SHEN,C.H.CHEN,D.BARILLA,Y.J.SUN,C.D.HSIAO JRNL TITL CHROMOSOME SEGREGATION IN ARCHAEA: SEGA- AND SEGB-DNA JRNL TITL 2 COMPLEX STRUCTURES PROVIDE INSIGHTS INTO SEGROSOME ASSEMBLY. JRNL REF NUCLEIC ACIDS RES. V. 49 13150 2021 JRNL REFN ESSN 1362-4962 JRNL PMID 34850144 JRNL DOI 10.1093/NAR/GKAB1155 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 13743 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1375 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 26.9100 - 4.5200 1.00 1361 152 0.1819 0.2148 REMARK 3 2 4.5200 - 3.5900 1.00 1290 142 0.1647 0.1874 REMARK 3 3 3.5900 - 3.1400 1.00 1295 145 0.1844 0.2505 REMARK 3 4 3.1400 - 2.8500 1.00 1262 140 0.1855 0.2221 REMARK 3 5 2.8500 - 2.6500 1.00 1275 141 0.2077 0.2411 REMARK 3 6 2.6500 - 2.4900 1.00 1260 140 0.2024 0.2531 REMARK 3 7 2.4900 - 2.3700 1.00 1252 140 0.2117 0.2696 REMARK 3 8 2.3700 - 2.2600 0.99 1251 139 0.2143 0.2892 REMARK 3 9 2.2600 - 2.1800 0.92 1146 127 0.2083 0.2791 REMARK 3 10 2.1800 - 2.1000 0.78 976 109 0.2318 0.2695 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.760 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.30 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7DUT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1300020149. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-19 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 : NSRRC REMARK 200 BEAMLINE : BL15A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14301 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.63100 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: PHASER REMARK 200 STARTING MODEL: 6IUB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MES SODIUM SALT PH 6.5, PEG8000, REMARK 280 CALCIUM ACETATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 32.62550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.62550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 25.24050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 71.47350 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 25.24050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 71.47350 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 32.62550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 25.24050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 71.47350 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 32.62550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 25.24050 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 71.47350 REMARK 290 SMTRY3 8 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 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 APPLY THE FOLLOWING TO CHAINS: A 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 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 510 DISTANCE = 5.98 ANGSTROMS REMARK 525 HOH A 511 DISTANCE = 6.48 ANGSTROMS REMARK 525 HOH A 512 DISTANCE = 7.78 ANGSTROMS 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 MG A 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 15 OG1 REMARK 620 2 ADP A 301 O1B 81.2 REMARK 620 3 HOH A 404 O 80.7 80.2 REMARK 620 4 HOH A 407 O 160.9 83.4 107.9 REMARK 620 5 HOH A 410 O 82.9 163.6 93.0 112.9 REMARK 620 6 HOH A 437 O 77.1 99.0 157.6 94.2 81.5 REMARK 620 N 1 2 3 4 5 DBREF 7DUT A 1 220 UNP Q981B3 Q981B3_SACS2 1 220 SEQRES 1 A 220 MET ILE VAL THR VAL ILE ASN GLN LYS GLY GLY VAL GLY SEQRES 2 A 220 LYS THR THR THR SER VAL ASN LEU SER TYR TYR LEU SER SEQRES 3 A 220 LYS GLU LYS LYS THR GLY LEU LEU ASP LEU ASP PRO GLU SEQRES 4 A 220 GLY GLY ALA THR ILE SER TYR GLY MET LYS ARG GLU LEU SEQRES 5 A 220 LYS GLU LEU PRO LEU GLY GLU LYS SER VAL ASN ILE PHE SEQRES 6 A 220 ASN VAL GLU VAL PHE PRO ALA HIS ILE GLY LEU LEU LYS SEQRES 7 A 220 LEU GLU LEU ASN GLY ASP VAL GLU GLU ILE SER ASN LYS SEQRES 8 A 220 ILE LYS GLU ILE GLY LYS GLN PHE ASP PHE LEU VAL ILE SEQRES 9 A 220 ASP THR PRO PRO ASN LEU GLY THR LEU ALA ILE SER ALA SEQRES 10 A 220 MET LEU VAL ALA ASP ARG ILE VAL SER PRO VAL THR PRO SEQRES 11 A 220 GLN PRO LEU ALA LEU GLU ALA ILE LYS ASN LEU ASP SER SEQRES 12 A 220 ARG LEU LYS SER ILE GLY LYS ASN ALA TYR SER PHE THR SEQRES 13 A 220 ASN PHE SER LYS LYS VAL VAL LYS LEU ASP ASN LEU SER SEQRES 14 A 220 SER VAL LYS PHE THR GLU ILE THR ILE PRO PRO SER ARG SEQRES 15 A 220 LEU PHE ILE GLU ALA SER ARG LEU GLY VAL PRO ALA LEU SEQRES 16 A 220 ARG TYR GLU GLU VAL ARG ILE LYS LYS PRO LYS LEU ALA SEQRES 17 A 220 ASN TYR TYR GLN GLN LEU ALA LYS VAL ILE SER GLU HET ADP A 301 27 HET MG A 302 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 MG MG 2+ FORMUL 4 HOH *112(H2 O) HELIX 1 AA1 GLY A 13 LYS A 27 1 15 HELIX 2 AA2 GLY A 40 TYR A 46 1 7 HELIX 3 AA3 ILE A 74 GLY A 83 1 10 HELIX 4 AA4 ASP A 84 LYS A 97 1 14 HELIX 5 AA5 GLY A 111 VAL A 120 1 10 HELIX 6 AA6 GLN A 131 GLY A 149 1 19 HELIX 7 AA7 SER A 181 GLY A 191 1 11 HELIX 8 AA8 PRO A 193 ILE A 202 1 10 HELIX 9 AA9 LYS A 206 GLU A 220 1 15 SHEET 1 AA1 8 VAL A 62 ILE A 64 0 SHEET 2 AA1 8 VAL A 67 PHE A 70 -1 O VAL A 69 N VAL A 62 SHEET 3 AA1 8 THR A 31 ASP A 35 1 N LEU A 33 O PHE A 70 SHEET 4 AA1 8 PHE A 101 ASP A 105 1 O VAL A 103 N GLY A 32 SHEET 5 AA1 8 ILE A 2 VAL A 5 1 N VAL A 3 O LEU A 102 SHEET 6 AA1 8 ARG A 123 VAL A 128 1 O ARG A 123 N THR A 4 SHEET 7 AA1 8 ALA A 152 ASN A 157 1 O TYR A 153 N ILE A 124 SHEET 8 AA1 8 VAL A 171 ILE A 178 1 O THR A 174 N SER A 154 LINK OG1 THR A 15 MG MG A 302 1555 1555 2.28 LINK O1B ADP A 301 MG MG A 302 1555 1555 2.42 LINK MG MG A 302 O HOH A 404 1555 1555 2.52 LINK MG MG A 302 O HOH A 407 1555 1555 2.39 LINK MG MG A 302 O HOH A 410 1555 1555 2.35 LINK MG MG A 302 O HOH A 437 1555 1555 2.47 CRYST1 50.481 142.947 65.251 90.00 90.00 90.00 C 2 2 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 0.019809 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006996 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015325 0.00000