HEADER DNA BINDING PROTEIN 11-FEB-16 5I41 TITLE STRUCTURE OF THE APO RACA DNA BINDING DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHROMOSOME-ANCHORING PROTEIN RACA; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: RACA, YWKC, BSU37030; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RACA, AXIAL FILAMENT, SPORULATION, B. SUBTILIS, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.A.SCHUMACHER REVDAT 3 06-MAR-24 5I41 1 JRNL REMARK REVDAT 2 29-JUN-16 5I41 1 JRNL REVDAT 1 04-MAY-16 5I41 0 JRNL AUTH M.A.SCHUMACHER,J.LEE,W.ZENG JRNL TITL MOLECULAR INSIGHTS INTO DNA BINDING AND ANCHORING BY THE JRNL TITL 2 BACILLUS SUBTILIS SPORULATION KINETOCHORE-LIKE RACA PROTEIN. JRNL REF NUCLEIC ACIDS RES. V. 44 5438 2016 JRNL REFN ESSN 1362-4962 JRNL PMID 27085804 JRNL DOI 10.1093/NAR/GKW248 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 4854 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.870 REMARK 3 FREE R VALUE TEST SET COUNT : 479 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 24.1511 - 2.5959 0.99 1531 163 0.1748 0.2075 REMARK 3 2 2.5959 - 2.0608 0.98 1448 164 0.1719 0.2075 REMARK 3 3 2.0608 - 1.8004 0.97 1396 152 0.2129 0.2479 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 0.50 REMARK 3 SHRINKAGE RADIUS : 0.16 REMARK 3 K_SOL : 0.45 REMARK 3 B_SOL : 62.27 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.670 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.04560 REMARK 3 B22 (A**2) : -2.31620 REMARK 3 B33 (A**2) : 1.27060 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 : 0.003 533 REMARK 3 ANGLE : 0.550 720 REMARK 3 CHIRALITY : 0.042 84 REMARK 3 PLANARITY : 0.002 92 REMARK 3 DIHEDRAL : 14.705 200 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN B AND RESID -1:27) REMARK 3 ORIGIN FOR THE GROUP (A): -6.2396 5.8863 -9.5349 REMARK 3 T TENSOR REMARK 3 T11: 0.0715 T22: 0.0850 REMARK 3 T33: 0.0928 T12: -0.0101 REMARK 3 T13: -0.0125 T23: 0.0016 REMARK 3 L TENSOR REMARK 3 L11: 0.1823 L22: 0.4324 REMARK 3 L33: 0.5209 L12: -0.0242 REMARK 3 L13: 0.0895 L23: -0.3389 REMARK 3 S TENSOR REMARK 3 S11: 0.0213 S12: -0.0588 S13: 0.0113 REMARK 3 S21: 0.1038 S22: -0.0407 S23: -0.1086 REMARK 3 S31: -0.1231 S32: 0.0547 S33: 0.0067 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN B AND RESID 28:38) REMARK 3 ORIGIN FOR THE GROUP (A): -14.1254 13.6213 -12.0041 REMARK 3 T TENSOR REMARK 3 T11: 0.2103 T22: 0.1380 REMARK 3 T33: 0.1267 T12: 0.0399 REMARK 3 T13: 0.0008 T23: 0.0206 REMARK 3 L TENSOR REMARK 3 L11: 0.0338 L22: 0.0387 REMARK 3 L33: 0.0343 L12: -0.0353 REMARK 3 L13: -0.0008 L23: 0.0066 REMARK 3 S TENSOR REMARK 3 S11: -0.1358 S12: -0.0671 S13: -0.0381 REMARK 3 S21: 0.5015 S22: 0.0654 S23: 0.0478 REMARK 3 S31: -0.3129 S32: -0.2378 S33: 0.0003 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN B AND RESID 39:49) REMARK 3 ORIGIN FOR THE GROUP (A): -2.9104 9.4516 -2.0227 REMARK 3 T TENSOR REMARK 3 T11: 0.1150 T22: 0.1078 REMARK 3 T33: 0.0908 T12: 0.0006 REMARK 3 T13: -0.0253 T23: -0.0142 REMARK 3 L TENSOR REMARK 3 L11: 0.6457 L22: 0.3479 REMARK 3 L33: 1.4038 L12: 0.3122 REMARK 3 L13: 0.3092 L23: 0.3445 REMARK 3 S TENSOR REMARK 3 S11: -0.1353 S12: -0.0138 S13: 0.1618 REMARK 3 S21: -0.0928 S22: -0.0924 S23: 0.1170 REMARK 3 S31: -0.3644 S32: -0.0236 S33: -0.2813 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN B AND RESID 50:65) REMARK 3 ORIGIN FOR THE GROUP (A): -1.1551 -1.9145 2.1291 REMARK 3 T TENSOR REMARK 3 T11: 0.1091 T22: 0.0893 REMARK 3 T33: 0.1030 T12: 0.0179 REMARK 3 T13: 0.0331 T23: -0.0105 REMARK 3 L TENSOR REMARK 3 L11: 0.0624 L22: 0.1867 REMARK 3 L33: 0.1214 L12: -0.1068 REMARK 3 L13: 0.0521 L23: -0.1421 REMARK 3 S TENSOR REMARK 3 S11: -0.1402 S12: -0.1401 S13: 0.0184 REMARK 3 S21: 0.1464 S22: 0.0448 S23: -0.1015 REMARK 3 S31: 0.0805 S32: 0.0740 S33: -0.0063 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 5I41 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1000218236. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-APR-15 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 : 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) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4854 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 24.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: 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 (%): 25.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM TRIS PH 7.5, 100 MM NACL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 16.89000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.32950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.26800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 21.32950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.89000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 17.26800 REMARK 290 SMTRY3 4 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: 4530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 GLY B -2 REMARK 465 LYS B 66 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 HIS B 0 -153.72 -131.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5I44 RELATED DB: PDB DBREF 5I41 B 1 66 UNP P45870 RACA_BACSU 1 66 SEQADV 5I41 GLY B -2 UNP P45870 EXPRESSION TAG SEQADV 5I41 SER B -1 UNP P45870 EXPRESSION TAG SEQADV 5I41 HIS B 0 UNP P45870 EXPRESSION TAG SEQADV 5I41 LYS B 50 UNP P45870 GLN 50 CONFLICT SEQRES 1 B 69 GLY SER HIS MET ASN THR ASN MET VAL ALA SER GLU LEU SEQRES 2 B 69 GLY VAL SER ALA LYS THR VAL GLN ARG TRP VAL LYS GLN SEQRES 3 B 69 LEU ASN LEU PRO ALA GLU ARG ASN GLU LEU GLY HIS TYR SEQRES 4 B 69 SER PHE THR ALA GLU ASP VAL LYS VAL LEU LYS SER VAL SEQRES 5 B 69 LYS LYS GLN ILE SER GLU GLY THR ALA ILE GLN ASP ILE SEQRES 6 B 69 HIS LEU PRO LYS FORMUL 2 HOH *53(H2 O) HELIX 1 AA1 THR B 3 GLY B 11 1 9 HELIX 2 AA2 SER B 13 LEU B 24 1 12 HELIX 3 AA3 THR B 39 GLU B 55 1 17 HELIX 4 AA4 ALA B 58 ILE B 62 5 5 SHEET 1 AA1 3 MET B 1 ASN B 2 0 SHEET 2 AA1 3 TYR B 36 PHE B 38 -1 O PHE B 38 N MET B 1 SHEET 3 AA1 3 GLU B 29 ARG B 30 -1 N GLU B 29 O SER B 37 CRYST1 33.780 34.536 42.659 90.00 90.00 90.00 P 21 21 21 4 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 0.029603 0.000000 0.000000 0.00000 SCALE2 0.000000 0.028955 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023442 0.00000