HEADER CELL CYCLE 04-DEC-18 6IVH TITLE CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF SCPA DERIVED FROM TITLE 2 THERMOCOCCUS ONNURINEUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SEGREGATION AND CONDENSATION PROTEIN A; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS ONNURINEUS (STRAIN NA1); SOURCE 3 ORGANISM_TAXID: 523850; SOURCE 4 STRAIN: NA1; SOURCE 5 GENE: TON_1071; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS CYTOSOLIC PROTEIN, CONDENSIN, KLEISIN, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR J.-H.JEON,H.-C.SHIN,B.-H.OH REVDAT 1 22-JAN-20 6IVH 0 JRNL AUTH J.-H.JEON,H.-S.LEE,H.-C.SHIN,M.-J.KWAK,Y.-K.KIM,S.GRUBER, JRNL AUTH 2 B.-H.OH JRNL TITL ARCHAEAL SMC-BASED CONDENSIN LACKING KITE SUBUNITS JRNL REF IUCRJ 2020 JRNL REFN ESSN 2052-2525 JRNL DOI 10.1107/S2052252519016634 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.750 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 8904 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.242 REMARK 3 R VALUE (WORKING SET) : 0.239 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.910 REMARK 3 FREE R VALUE TEST SET COUNT : 882 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 38.4965 - 4.5408 1.00 1367 149 0.2317 0.2100 REMARK 3 2 4.5408 - 3.6051 1.00 1363 162 0.2050 0.2303 REMARK 3 3 3.6051 - 3.1496 0.99 1377 155 0.2348 0.3018 REMARK 3 4 3.1496 - 2.8617 0.98 1357 139 0.2653 0.2856 REMARK 3 5 2.8617 - 2.6567 0.95 1302 149 0.2768 0.3322 REMARK 3 6 2.6567 - 2.5001 0.91 1256 128 0.3080 0.3441 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.12 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.51 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 : 0.004 776 REMARK 3 ANGLE : 0.732 1047 REMARK 3 CHIRALITY : 0.046 126 REMARK 3 PLANARITY : 0.002 131 REMARK 3 DIHEDRAL : 19.185 489 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: THE STRUCTURE FACTOR FILE CONTAINS REMARK 3 FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS REMARK 4 REMARK 4 6IVH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-DEC-18. REMARK 100 THE DEPOSITION ID IS D_1300010006. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) 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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8911 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.27900 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: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTAL GROWTH AT 3.5 M SODIUM FORMATE REMARK 280 AND 0.1 M SODIUM MALONATE, DEHYDRATION FOR 2 H IN THE RESERVOIR REMARK 280 SOLUTION CONTAINING ADDITIONAL 10% GLYCEROL, PH 7.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 13.31133 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 26.62267 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 19.96700 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 33.27833 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 6.65567 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 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 MSE A 1 REMARK 465 GLU A 2 REMARK 465 SER A 3 REMARK 465 ARG A 4 REMARK 465 ARG A 5 REMARK 465 ASP A 75 REMARK 465 GLU A 76 REMARK 465 GLU A 77 REMARK 465 ASP A 78 REMARK 465 GLU A 79 REMARK 465 GLU A 80 REMARK 465 GLU A 81 REMARK 465 LYS A 82 REMARK 465 HIS A 83 REMARK 465 GLU A 84 REMARK 465 GLU A 85 REMARK 465 HIS A 86 REMARK 465 ILE A 87 REMARK 465 ARG A 88 REMARK 465 VAL A 89 REMARK 465 GLU A 90 REMARK 465 VAL A 91 REMARK 465 GLU A 92 REMARK 465 PRO A 93 REMARK 465 LEU A 94 REMARK 465 ALA A 95 REMARK 465 PRO A 96 REMARK 465 GLU A 122 REMARK 465 LYS A 123 REMARK 465 ARG A 124 REMARK 465 LYS A 125 REMARK 465 PRO A 126 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD1 ASP A 25 NH2 ARG A 100 4665 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 99 163.78 178.60 REMARK 500 REMARK 500 REMARK: NULL DBREF 6IVH A 1 126 UNP B6YWU6 B6YWU6_THEON 1 126 SEQRES 1 A 126 MSE GLU SER ARG ARG GLU GLU GLU ILE THR PRO VAL ASP SEQRES 2 A 126 ILE LEU LEU GLN LEU VAL GLN MSE GLY LYS VAL ASP PRO SEQRES 3 A 126 TRP ASN ILE ASP ILE VAL ASP LEU THR GLU LYS TYR ILE SEQRES 4 A 126 GLU ARG LEU ARG GLU MSE LYS GLU LEU ASP LEU ARG VAL SEQRES 5 A 126 SER ALA ARG ALA ILE LEU ALA ALA SER ILE LEU VAL ARG SEQRES 6 A 126 MSE LYS SER GLU ALA LEU LEU TYR ALA ASP GLU GLU ASP SEQRES 7 A 126 GLU GLU GLU LYS HIS GLU GLU HIS ILE ARG VAL GLU VAL SEQRES 8 A 126 GLU PRO LEU ALA PRO PRO LEU ARG ARG VAL GLU ARG TYR SEQRES 9 A 126 TYR THR PHE ASP ASP LEU LEU ASP ALA LEU MSE ASP ALA SEQRES 10 A 126 LEU GLU GLU ALA GLU LYS ARG LYS PRO MODRES 6IVH MSE A 21 MET MODIFIED RESIDUE MODRES 6IVH MSE A 45 MET MODIFIED RESIDUE MODRES 6IVH MSE A 66 MET MODIFIED RESIDUE MODRES 6IVH MSE A 115 MET MODIFIED RESIDUE HET MSE A 21 8 HET MSE A 45 8 HET MSE A 66 8 HET MSE A 115 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 2 HOH *(H2 O) HELIX 1 AA1 THR A 10 MSE A 21 1 12 HELIX 2 AA2 ILE A 31 LEU A 48 1 18 HELIX 3 AA3 SER A 53 TYR A 73 1 21 HELIX 4 AA4 THR A 106 ALA A 121 1 16 SHEET 1 AA1 2 ILE A 29 ASP A 30 0 SHEET 2 AA1 2 TYR A 104 TYR A 105 -1 O TYR A 105 N ILE A 29 LINK C GLN A 20 N MSE A 21 1555 1555 1.33 LINK C MSE A 21 N GLY A 22 1555 1555 1.33 LINK C GLU A 44 N MSE A 45 1555 1555 1.33 LINK C MSE A 45 N LYS A 46 1555 1555 1.34 LINK C ARG A 65 N MSE A 66 1555 1555 1.33 LINK C MSE A 66 N LYS A 67 1555 1555 1.33 LINK C LEU A 114 N MSE A 115 1555 1555 1.33 LINK C MSE A 115 N ASP A 116 1555 1555 1.34 CISPEP 1 GLU A 6 GLU A 7 0 -7.00 CRYST1 76.984 76.984 39.934 90.00 90.00 120.00 P 61 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 0.012990 0.007500 0.000000 0.00000 SCALE2 0.000000 0.014999 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025041 0.00000