HEADER REPLICATION 11-SEP-15 5DOL TITLE CRYSTAL STRUCTURE OF YABA AMINO-TERMINAL DOMAIN FROM BACILLUS SUBTILIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: INITIATION-CONTROL PROTEIN YABA; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 1-62; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: AMINO-TERMINAL DOMAIN OF THE PROTEIN (RESIDUS 1-62) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS (STRAIN 168); SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 GENE: YABA, BSU00330; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET151/D-TOPO KEYWDS YABA, DNAA, DNAN, ZINC FINGER, INITIATION CONTROL, REPLICATION EXPDTA X-RAY DIFFRACTION AUTHOR M.V.CHERRIER,A.BAZIN,K.H.JAMESON,A.J.WILKINSON,M.F.NOIROT-GROS, AUTHOR 2 L.TERRADOT REVDAT 2 08-MAY-24 5DOL 1 REMARK REVDAT 1 20-JAN-16 5DOL 0 JRNL AUTH L.FELICORI,K.H.JAMESON,P.ROBLIN,M.J.FOGG,T.GARCIA-GARCIA, JRNL AUTH 2 M.VENTROUX,M.V.CHERRIER,A.BAZIN,P.NOIROT,A.J.WILKINSON, JRNL AUTH 3 F.MOLINA,L.TERRADOT,M.F.NOIROT-GROS JRNL TITL TETRAMERIZATION AND INTERDOMAIN FLEXIBILITY OF THE JRNL TITL 2 REPLICATION INITIATION CONTROLLER YABA ENABLES SIMULTANEOUS JRNL TITL 3 BINDING TO MULTIPLE PARTNERS. JRNL REF NUCLEIC ACIDS RES. V. 44 449 2016 JRNL REFN ESSN 1362-4962 JRNL PMID 26615189 JRNL DOI 10.1093/NAR/GKV1318 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 7301 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.970 REMARK 3 FREE R VALUE TEST SET COUNT : 728 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 36.1000 - 4.6146 0.93 1295 143 0.2106 0.2414 REMARK 3 2 4.6146 - 3.6639 1.00 1341 150 0.1910 0.2488 REMARK 3 3 3.6639 - 3.2011 1.00 1311 146 0.2486 0.3313 REMARK 3 4 3.2011 - 2.9085 1.00 1325 146 0.2848 0.3472 REMARK 3 5 2.9085 - 2.7002 1.00 1301 143 0.3460 0.3911 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) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 90.05 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 125.3 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 : 0.005 1081 REMARK 3 ANGLE : 0.616 1448 REMARK 3 CHIRALITY : 0.023 156 REMARK 3 PLANARITY : 0.002 191 REMARK 3 DIHEDRAL : 14.831 432 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 62 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.2596 107.0581 70.1872 REMARK 3 T TENSOR REMARK 3 T11: 0.4798 T22: 1.1559 REMARK 3 T33: 0.8870 T12: 0.0500 REMARK 3 T13: 0.0421 T23: 0.0457 REMARK 3 L TENSOR REMARK 3 L11: 3.7408 L22: 3.7235 REMARK 3 L33: 1.8384 L12: -3.5748 REMARK 3 L13: 1.7242 L23: -0.2875 REMARK 3 S TENSOR REMARK 3 S11: 0.3047 S12: -1.2845 S13: -0.8663 REMARK 3 S21: -0.2095 S22: 0.1948 S23: 0.1333 REMARK 3 S31: 0.1370 S32: 0.3364 S33: -0.4237 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 62 ) REMARK 3 ORIGIN FOR THE GROUP (A): -32.7307 129.3694 66.2272 REMARK 3 T TENSOR REMARK 3 T11: 0.7601 T22: 0.8103 REMARK 3 T33: 0.8637 T12: 0.0055 REMARK 3 T13: 0.1727 T23: 0.0305 REMARK 3 L TENSOR REMARK 3 L11: 5.5022 L22: 6.2092 REMARK 3 L33: 3.5117 L12: -6.6258 REMARK 3 L13: 2.9275 L23: -2.0880 REMARK 3 S TENSOR REMARK 3 S11: -0.5536 S12: -1.4007 S13: -0.0251 REMARK 3 S21: 0.3327 S22: 0.7924 S23: -0.1292 REMARK 3 S31: -0.6438 S32: -0.5547 S33: -0.3544 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 5DOL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000213545. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.93222 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7306 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 36.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 21.20 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : 0.07200 REMARK 200 FOR THE DATA SET : 17.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 23.00 REMARK 200 R MERGE FOR SHELL (I) : 2.62600 REMARK 200 R SYM FOR SHELL (I) : 1.45000 REMARK 200 FOR SHELL : 1.230 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHASER 2.5.6, SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350 (W/V), 100 MM BIS-TRIS REMARK 280 PROPANE PH 6.5, 200 MM POTASSIUM THIOCYANATE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 43.14000 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 21.57000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 21.57000 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 43.14000 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 CYCLIC POINT SYMMETRY (SCHOENFLIES SYMBOL = C2). 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -88.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 BIOMT1 2 -0.500000 0.866025 0.000000 -125.22000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 72.29580 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 129.42000 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 MET A 1 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 3 CG CD CE NZ REMARK 480 GLU A 5 CG CD OE1 OE2 REMARK 480 LYS A 28 NZ REMARK 480 GLU A 36 CG CD OE1 OE2 REMARK 480 GLU A 37 CD OE1 OE2 REMARK 480 LYS A 46 CD CE NZ REMARK 480 GLN A 57 CG CD OE1 NE2 REMARK 480 GLU A 60 CG CD OE1 OE2 REMARK 480 LYS A 61 CB CG CD CE NZ REMARK 480 MET B 1 CB CG SD CE REMARK 480 ASP B 2 CB CG OD1 OD2 REMARK 480 LYS B 4 CB CG CD CE NZ REMARK 480 ASP B 8 OD1 OD2 REMARK 480 GLU B 15 CG CD OE1 OE2 REMARK 480 ARG B 22 CG CD NE REMARK 480 LYS B 46 CD CE NZ REMARK 480 ASP B 53 CG OD1 OD2 REMARK 480 ASP B 54 CG OD1 OD2 REMARK 480 GLN B 57 CD OE1 NE2 REMARK 480 GLU B 60 CG CD OE1 OE2 REMARK 480 LYS B 61 CG CD CE NZ 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 NH1 ARG A 49 OE2 GLU B 44 4467 2.19 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 LYS B 3 -103.96 -122.40 REMARK 500 REMARK 500 REMARK: NULL DBREF 5DOL A 1 62 UNP P37542 YABA_BACSU 1 62 DBREF 5DOL B 1 62 UNP P37542 YABA_BACSU 1 62 SEQRES 1 A 62 MET ASP LYS LYS GLU LEU PHE ASP THR VAL ILE ASN LEU SEQRES 2 A 62 GLU GLU GLN ILE GLY SER LEU TYR ARG GLN LEU GLY ASP SEQRES 3 A 62 LEU LYS GLN HIS ILE GLY GLU MET ILE GLU GLU ASN HIS SEQRES 4 A 62 HIS LEU GLN LEU GLU ASN LYS HIS LEU ARG LYS ARG LEU SEQRES 5 A 62 ASP ASP THR THR GLN GLN ILE GLU LYS PHE SEQRES 1 B 62 MET ASP LYS LYS GLU LEU PHE ASP THR VAL ILE ASN LEU SEQRES 2 B 62 GLU GLU GLN ILE GLY SER LEU TYR ARG GLN LEU GLY ASP SEQRES 3 B 62 LEU LYS GLN HIS ILE GLY GLU MET ILE GLU GLU ASN HIS SEQRES 4 B 62 HIS LEU GLN LEU GLU ASN LYS HIS LEU ARG LYS ARG LEU SEQRES 5 B 62 ASP ASP THR THR GLN GLN ILE GLU LYS PHE FORMUL 3 HOH *4(H2 O) HELIX 1 AA1 ASP A 2 PHE A 62 1 61 HELIX 2 AA2 LYS B 3 GLU B 60 1 58 CRYST1 83.480 83.480 64.710 90.00 90.00 120.00 P 32 2 1 12 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 0.011979 0.006916 0.000000 0.00000 SCALE2 0.000000 0.013832 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015454 0.00000