HEADER DNA BINDING PROTEIN 20-DEC-16 5UBE TITLE CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN (DOMAIN 1) OF RCTB COMPND MOL_ID: 1; COMPND 2 MOLECULE: RCTB REPLICATION INITIATOR PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: DOMAIN 1 (UNP RESIDUES 1-124); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE; SOURCE 3 ORGANISM_TAXID: 666; SOURCE 4 GENE: DN30_18, EN12_14105; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA REPLICATION INITIATION, DNA BINDING, SECONDARY CHROMOSOME, VIBRIO KEYWDS 2 CHOLERAE, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.ORLOVA,O.IVASHKIV,M.K.WALDOR,D.JERUZALMI REVDAT 5 04-OCT-23 5UBE 1 REMARK REVDAT 4 01-JAN-20 5UBE 1 REMARK REVDAT 3 27-SEP-17 5UBE 1 REMARK REVDAT 2 03-MAY-17 5UBE 1 JRNL REVDAT 1 11-JAN-17 5UBE 0 JRNL AUTH N.ORLOVA,M.GERDING,O.IVASHKIV,P.D.B.OLINARES,B.T.CHAIT, JRNL AUTH 2 M.K.WALDOR,D.JERUZALMI JRNL TITL THE REPLICATION INITIATOR OF THE CHOLERA PATHOGEN'S SECOND JRNL TITL 2 CHROMOSOME SHOWS STRUCTURAL SIMILARITY TO PLASMID JRNL TITL 3 INITIATORS. JRNL REF NUCLEIC ACIDS RES. V. 45 3724 2017 JRNL REFN ESSN 1362-4962 JRNL PMID 28031373 JRNL DOI 10.1093/NAR/GKW1288 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11_2567 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.33 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 78.1 REMARK 3 NUMBER OF REFLECTIONS : 15588 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.231 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1561 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 33.3306 - 4.4442 0.82 1397 156 0.2030 0.2121 REMARK 3 2 4.4442 - 3.5288 0.81 1316 147 0.2046 0.2391 REMARK 3 3 3.5288 - 3.0831 0.86 1423 158 0.2413 0.2726 REMARK 3 4 3.0831 - 2.8013 0.89 1467 161 0.2348 0.3076 REMARK 3 5 2.8013 - 2.6006 0.88 1428 161 0.2375 0.3133 REMARK 3 6 2.6006 - 2.4474 0.87 1392 154 0.2524 0.2923 REMARK 3 7 2.4474 - 2.3248 0.81 1317 147 0.2475 0.3212 REMARK 3 8 2.3248 - 2.2237 0.78 1270 143 0.2609 0.3149 REMARK 3 9 2.2237 - 2.1381 0.70 1124 127 0.2664 0.2946 REMARK 3 10 2.1381 - 2.0643 0.63 1013 113 0.2743 0.3494 REMARK 3 11 2.0643 - 1.9998 0.54 880 94 0.3042 0.3643 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.006 1874 REMARK 3 ANGLE : 0.757 2526 REMARK 3 CHIRALITY : 0.045 296 REMARK 3 PLANARITY : 0.004 322 REMARK 3 DIHEDRAL : 11.849 1140 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 5UBE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1000224995. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUL-14 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 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 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 V714 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 V714 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16800 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 84.3 REMARK 200 DATA REDUNDANCY : 1.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05700 REMARK 200 FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 64.6 REMARK 200 DATA REDUNDANCY IN SHELL : 1.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 16.60 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 1.11_2567-000 REMARK 200 STARTING MODEL: 5UBD REMARK 200 REMARK 200 REMARK: PLATE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS OF RCTB DOMAIN 1 (1-124) WERE REMARK 280 PREPARED USING THE SITTING DROP VAPOR DIFFUSION METHOD BY MIXING REMARK 280 0.1, OR 0.2, OR 0.4 UL OF THE PROTEIN SOLUTION (22.4 MG/ML RCTB- REMARK 280 2-124 IN 20 MM TRIS PH 7.4, 50 MM SODIUM CHLORIDE, 5% GLYCEROL, REMARK 280 5 MM 2-MERCAPTOETHANOL) AND 0.2 UL OF RESERVOIR SOLUTION (0.24 M REMARK 280 SODIUM MALONATE PH 7.0, 20% W/V PEG 3350)., VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 26.06350 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 MET A 1 REMARK 465 SER A 2 REMARK 465 SER A 3 REMARK 465 GLU A 4 REMARK 465 GLU A 5 REMARK 465 LYS A 6 REMARK 465 VAL A 123 REMARK 465 LEU A 124 REMARK 465 HIS A 125 REMARK 465 HIS A 126 REMARK 465 HIS A 127 REMARK 465 HIS A 128 REMARK 465 HIS A 129 REMARK 465 HIS A 130 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 SER B 3 REMARK 465 GLU B 4 REMARK 465 GLU B 5 REMARK 465 LYS B 6 REMARK 465 VAL B 123 REMARK 465 LEU B 124 REMARK 465 HIS B 125 REMARK 465 HIS B 126 REMARK 465 HIS B 127 REMARK 465 HIS B 128 REMARK 465 HIS B 129 REMARK 465 HIS B 130 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 247 O HOH B 212 1.85 REMARK 500 NE2 GLN A 83 O HOH A 201 2.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5UBD RELATED DB: PDB REMARK 900 RELATED ID: 5UBF RELATED DB: PDB DBREF1 5UBE A 1 124 UNP A0A085QGR2_VIBCL DBREF2 5UBE A A0A085QGR2 1 124 DBREF1 5UBE B 1 124 UNP A0A085QGR2_VIBCL DBREF2 5UBE B A0A085QGR2 1 124 SEQADV 5UBE HIS A 125 UNP A0A085QGR EXPRESSION TAG SEQADV 5UBE HIS A 126 UNP A0A085QGR EXPRESSION TAG SEQADV 5UBE HIS A 127 UNP A0A085QGR EXPRESSION TAG SEQADV 5UBE HIS A 128 UNP A0A085QGR EXPRESSION TAG SEQADV 5UBE HIS A 129 UNP A0A085QGR EXPRESSION TAG SEQADV 5UBE HIS A 130 UNP A0A085QGR EXPRESSION TAG SEQADV 5UBE HIS B 125 UNP A0A085QGR EXPRESSION TAG SEQADV 5UBE HIS B 126 UNP A0A085QGR EXPRESSION TAG SEQADV 5UBE HIS B 127 UNP A0A085QGR EXPRESSION TAG SEQADV 5UBE HIS B 128 UNP A0A085QGR EXPRESSION TAG SEQADV 5UBE HIS B 129 UNP A0A085QGR EXPRESSION TAG SEQADV 5UBE HIS B 130 UNP A0A085QGR EXPRESSION TAG SEQRES 1 A 130 MET SER SER GLU GLU LYS ARG LEU ILE LYS LEU PRO ARG SEQRES 2 A 130 THR HIS LYS ASP GLY HIS LEU PHE GLU VAL SER GLU ALA SEQRES 3 A 130 ALA ILE ASP TRP ILE GLU GLN TYR GLN HIS PHE LYS GLY SEQRES 4 A 130 VAL THR LYS SER ILE VAL GLU LEU LEU ASN LEU ILE SER SEQRES 5 A 130 LEU ARG GLY LEU ARG SER ARG ASP GLY LEU VAL SER THR SEQRES 6 A 130 THR GLU LEU ILE ASP ALA THR ASP GLY GLN LEU THR ARG SEQRES 7 A 130 ALA ALA ILE GLN GLN ARG LEU ARG ALA ALA VAL ALA VAL SEQRES 8 A 130 GLY LEU PHE LYS GLN ILE PRO VAL ARG PHE GLU GLU GLY SEQRES 9 A 130 LEU ALA GLY LYS THR MET LEU HIS ARG PHE ILE ASN PRO SEQRES 10 A 130 ASN GLN LEU ILE SER VAL LEU HIS HIS HIS HIS HIS HIS SEQRES 1 B 130 MET SER SER GLU GLU LYS ARG LEU ILE LYS LEU PRO ARG SEQRES 2 B 130 THR HIS LYS ASP GLY HIS LEU PHE GLU VAL SER GLU ALA SEQRES 3 B 130 ALA ILE ASP TRP ILE GLU GLN TYR GLN HIS PHE LYS GLY SEQRES 4 B 130 VAL THR LYS SER ILE VAL GLU LEU LEU ASN LEU ILE SER SEQRES 5 B 130 LEU ARG GLY LEU ARG SER ARG ASP GLY LEU VAL SER THR SEQRES 6 B 130 THR GLU LEU ILE ASP ALA THR ASP GLY GLN LEU THR ARG SEQRES 7 B 130 ALA ALA ILE GLN GLN ARG LEU ARG ALA ALA VAL ALA VAL SEQRES 8 B 130 GLY LEU PHE LYS GLN ILE PRO VAL ARG PHE GLU GLU GLY SEQRES 9 B 130 LEU ALA GLY LYS THR MET LEU HIS ARG PHE ILE ASN PRO SEQRES 10 B 130 ASN GLN LEU ILE SER VAL LEU HIS HIS HIS HIS HIS HIS FORMUL 3 HOH *64(H2 O) HELIX 1 AA1 THR A 14 GLY A 18 5 5 HELIX 2 AA2 GLU A 25 GLN A 35 1 11 HELIX 3 AA3 THR A 41 LEU A 56 1 16 HELIX 4 AA4 THR A 65 THR A 72 1 8 HELIX 5 AA5 THR A 77 GLY A 92 1 16 HELIX 6 AA6 ASN A 116 ILE A 121 1 6 HELIX 7 AA7 THR B 14 GLY B 18 5 5 HELIX 8 AA8 ALA B 26 GLN B 35 1 10 HELIX 9 AA9 THR B 41 LEU B 56 1 16 HELIX 10 AB1 THR B 65 ALA B 71 1 7 HELIX 11 AB2 THR B 77 VAL B 91 1 15 HELIX 12 AB3 ASN B 116 ILE B 121 1 6 SHEET 1 AA1 4 LEU A 62 SER A 64 0 SHEET 2 AA1 4 LEU A 20 GLU A 22 -1 N PHE A 21 O VAL A 63 SHEET 3 AA1 4 LYS A 108 PHE A 114 1 O MET A 110 N LEU A 20 SHEET 4 AA1 4 PHE A 94 ARG A 100 -1 N ILE A 97 O LEU A 111 SHEET 1 AA2 2 LEU B 8 ILE B 9 0 SHEET 2 AA2 2 ARG B 100 PHE B 101 1 O ARG B 100 N ILE B 9 SHEET 1 AA3 4 LEU B 62 SER B 64 0 SHEET 2 AA3 4 LEU B 20 GLU B 22 -1 N PHE B 21 O VAL B 63 SHEET 3 AA3 4 MET B 110 PHE B 114 1 O HIS B 112 N GLU B 22 SHEET 4 AA3 4 PHE B 94 PRO B 98 -1 N LYS B 95 O ARG B 113 CISPEP 1 LEU A 11 PRO A 12 0 5.08 CISPEP 2 LEU B 11 PRO B 12 0 1.21 CRYST1 45.803 52.127 63.414 90.00 101.61 90.00 P 1 21 1 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 0.021833 0.000000 0.004486 0.00000 SCALE2 0.000000 0.019184 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016099 0.00000