HEADER DNA BINDING PROTEIN 18-FEB-18 6CFY TITLE BOSEA SP ROOT 381 APO GAPR STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: UPF0335 PROTEIN ASE63_04290; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOSEA SP. ROOT381; SOURCE 3 ORGANISM_TAXID: 1736524; SOURCE 4 GENE: ASE63_04290; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CAULOBACTER, NAP, DNA BINDING, TOPOISOMERASE, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.A.SCHUMACHERR REVDAT 3 17-OCT-18 6CFY 1 JRNL REVDAT 2 03-OCT-18 6CFY 1 JRNL REVDAT 1 12-SEP-18 6CFY 0 JRNL AUTH M.S.GUO,D.L.HAAKONSEN,W.ZENG,M.A.SCHUMACHER,M.T.LAUB JRNL TITL A BACTERIAL CHROMOSOME STRUCTURING PROTEIN BINDS OVERTWISTED JRNL TITL 2 DNA TO STIMULATE TYPE II TOPOISOMERASES AND ENABLE DNA JRNL TITL 3 REPLICATION. JRNL REF CELL V. 175 583 2018 JRNL REFN ISSN 1097-4172 JRNL PMID 30220456 JRNL DOI 10.1016/J.CELL.2018.08.029 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6.4_486 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.790 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 12187 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1235 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 38.8767 - 4.9893 1.00 1209 137 0.2731 0.2613 REMARK 3 2 4.9893 - 3.9614 1.00 1209 138 0.1816 0.2253 REMARK 3 3 3.9614 - 3.4610 1.00 1252 138 0.2106 0.2733 REMARK 3 4 3.4610 - 3.1448 1.00 1203 136 0.1912 0.2818 REMARK 3 5 3.1448 - 2.9194 1.00 1214 140 0.2139 0.2682 REMARK 3 6 2.9194 - 2.7474 1.00 1229 135 0.2572 0.2841 REMARK 3 7 2.7474 - 2.6098 1.00 1203 135 0.2926 0.3210 REMARK 3 8 2.6098 - 2.4962 1.00 1220 137 0.3401 0.3748 REMARK 3 9 2.4962 - 2.4001 1.00 1213 139 0.3329 0.3465 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.95 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 81.29 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.440 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.030 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.41180 REMARK 3 B22 (A**2) : 3.41180 REMARK 3 B33 (A**2) : -6.82370 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.018 569 REMARK 3 ANGLE : 1.675 757 REMARK 3 CHIRALITY : 0.103 84 REMARK 3 PLANARITY : 0.007 99 REMARK 3 DIHEDRAL : 15.750 233 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): -0.8545 -16.4547 9.7667 REMARK 3 T TENSOR REMARK 3 T11: 0.3880 T22: 0.5721 REMARK 3 T33: 0.4802 T12: 0.0051 REMARK 3 T13: -0.0771 T23: -0.0266 REMARK 3 L TENSOR REMARK 3 L11: 0.1954 L22: 0.2181 REMARK 3 L33: 0.2481 L12: 0.1330 REMARK 3 L13: 0.2328 L23: 0.1520 REMARK 3 S TENSOR REMARK 3 S11: 0.0276 S12: -0.1724 S13: 0.0089 REMARK 3 S21: 0.1206 S22: -0.0450 S23: 0.0479 REMARK 3 S31: -0.0361 S32: 0.2061 S33: 0.0007 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 6CFY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1000232684. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-17 REMARK 200 TEMPERATURE (KELVIN) : 273 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12187 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 38.870 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09900 REMARK 200 FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 74.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% MPD, 10 MM MGCL2, HEPES (7.5) REMARK 280 0.001 M SPERMINE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 2 2 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 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+3/4 REMARK 290 8555 -Y,-X,-Z+1/4 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 102.56250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 51.28125 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 153.84375 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 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 102.56250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 153.84375 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 51.28125 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: 2430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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 0.00000 REMARK 350 BIOMT3 2 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 MSE A 1 REMARK 465 ASP A 2 REMARK 465 ASP A 3 REMARK 465 PRO A 4 REMARK 465 VAL A 5 REMARK 465 ALA A 6 REMARK 465 GLY A 7 REMARK 465 ASP A 8 REMARK 465 SER A 79 REMARK 465 ALA A 80 DBREF1 6CFY A 1 80 UNP A0A0Q9HY32_9BRAD DBREF2 6CFY A A0A0Q9HY32 1 80 SEQADV 6CFY MSE A 48 UNP A0A0Q9HY3 LEU 48 ENGINEERED MUTATION SEQADV 6CFY MSE A 54 UNP A0A0Q9HY3 ILE 54 ENGINEERED MUTATION SEQADV 6CFY MSE A 73 UNP A0A0Q9HY3 LEU 73 ENGINEERED MUTATION SEQRES 1 A 80 MSE ASP ASP PRO VAL ALA GLY ASP GLN LEU LYS SER ILE SEQRES 2 A 80 VAL GLU ARG ILE GLU ARG LEU GLU GLU GLU LYS LYS THR SEQRES 3 A 80 ILE ALA ASP ASP ILE LYS GLU VAL TYR ALA GLU ALA LYS SEQRES 4 A 80 GLY ASN GLY TYR ASP VAL LYS VAL MSE ARG LYS VAL ILE SEQRES 5 A 80 ALA MSE ARG LYS ARG ASP ALA ASN GLU ARG ALA GLU GLU SEQRES 6 A 80 GLU ALA ILE LEU ASP LEU TYR MSE GLN ALA VAL GLY GLU SEQRES 7 A 80 SER ALA HET MSE A 48 8 HET MSE A 54 8 HET MSE A 73 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 HOH *5(H2 O) HELIX 1 AA1 GLN A 9 ASN A 41 1 33 HELIX 2 AA2 ASP A 44 GLY A 77 1 34 LINK C VAL A 47 N MSE A 48 1555 1555 1.34 LINK C MSE A 48 N ARG A 49 1555 1555 1.34 LINK C ALA A 53 N MSE A 54 1555 1555 1.33 LINK C MSE A 54 N ARG A 55 1555 1555 1.33 LINK C TYR A 72 N MSE A 73 1555 1555 1.33 LINK C MSE A 73 N GLN A 74 1555 1555 1.33 CRYST1 39.589 39.589 205.125 90.00 90.00 90.00 P 41 2 2 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 0.025260 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025260 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004875 0.00000