HEADER CELL CYCLE 06-OCT-09 2WUK TITLE DIVIVA N-TERMINAL DOMAIN, F17A MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: SEPTUM SITE-DETERMINING PROTEIN DIVIVA; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN, RESIDUES 1-57; COMPND 5 SYNONYM: CELL DIVISION INITIATION PROTEIN DIVIVA, MINICELL-ASSOCIATED COMPND 6 PROTEIN DIVIVA; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 STRAIN: 168; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BACTERIAL CELL DIVISION, SEPTATION, CELL CYCLE, SPORULATION EXPDTA X-RAY DIFFRACTION AUTHOR M.A.OLIVA,T.A.LEONARD,J.LOWE REVDAT 3 08-MAY-24 2WUK 1 REMARK REVDAT 2 28-JUL-10 2WUK 1 JRNL REVDAT 1 09-JUN-10 2WUK 0 JRNL AUTH M.A.OLIVA,S.HALBEDEL,S.M.FREUND,P.DUTOW,T.A.LEONARD, JRNL AUTH 2 D.B.VEPRINTSEV,L.W.HAMOEN,J.LOWE JRNL TITL FEATURES CRITICAL FOR MEMBRANE BINDING REVEALED BY DIVIVA JRNL TITL 2 CRYSTAL STRUCTURE. JRNL REF EMBO J. V. 29 1988 2010 JRNL REFN ISSN 0261-4189 JRNL PMID 20502438 JRNL DOI 10.1038/EMBOJ.2010.99 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 30928 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1553 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 15.5518 - 4.2003 0.94 2608 132 0.1690 0.2341 REMARK 3 2 4.2003 - 3.3448 0.99 2727 137 0.1281 0.2071 REMARK 3 3 3.3448 - 2.9252 0.99 2699 165 0.1442 0.2264 REMARK 3 4 2.9252 - 2.6592 0.98 2739 137 0.1508 0.2119 REMARK 3 5 2.6592 - 2.4694 0.98 2689 155 0.1538 0.2440 REMARK 3 6 2.4694 - 2.3243 0.98 2714 129 0.1517 0.2366 REMARK 3 7 2.3243 - 2.2082 0.97 2622 162 0.1507 0.2751 REMARK 3 8 2.2082 - 2.1124 0.96 2687 167 0.1560 0.2210 REMARK 3 9 2.1124 - 2.0312 0.96 2592 139 0.1657 0.2682 REMARK 3 10 2.0312 - 1.9613 0.96 2707 113 0.1990 0.2721 REMARK 3 11 1.9613 - 1.9001 0.95 2591 117 0.2433 0.3272 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 : 0.38 REMARK 3 B_SOL : 60.14 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.800 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.85 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.05080 REMARK 3 B22 (A**2) : 0.37330 REMARK 3 B33 (A**2) : 0.67740 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.77030 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 : 0.007 1882 REMARK 3 ANGLE : 0.949 2535 REMARK 3 CHIRALITY : 0.060 281 REMARK 3 PLANARITY : 0.004 336 REMARK 3 DIHEDRAL : 16.283 745 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 2WUK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1290041341. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14059 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 21.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.20000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 14.28300 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, PHE 17 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN B, PHE 17 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN C, PHE 17 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN D, PHE 17 TO ALA 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 ILE A 57 REMARK 465 MET B 1 REMARK 465 ARG B 56 REMARK 465 ILE B 57 REMARK 465 MET C 1 REMARK 465 MET D 1 REMARK 465 ILE D 57 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 D 2027 O HOH D 2072 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 ASP B 54 32.29 -97.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2005 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH B2009 DISTANCE = 6.30 ANGSTROMS REMARK 525 HOH D2013 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH D2018 DISTANCE = 6.34 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WUJ RELATED DB: PDB REMARK 900 DIVIVA N-TERMINAL DOMAIN DBREF 2WUK A 1 57 UNP P71021 DIV4A_BACSU 1 57 DBREF 2WUK B 1 57 UNP P71021 DIV4A_BACSU 1 57 DBREF 2WUK C 1 57 UNP P71021 DIV4A_BACSU 1 57 DBREF 2WUK D 1 57 UNP P71021 DIV4A_BACSU 1 57 SEQADV 2WUK ALA A 17 UNP P71021 PHE 17 ENGINEERED MUTATION SEQADV 2WUK ALA B 17 UNP P71021 PHE 17 ENGINEERED MUTATION SEQADV 2WUK ALA C 17 UNP P71021 PHE 17 ENGINEERED MUTATION SEQADV 2WUK ALA D 17 UNP P71021 PHE 17 ENGINEERED MUTATION SEQRES 1 A 57 MET PRO LEU THR PRO ASN ASP ILE HIS ASN LYS THR PHE SEQRES 2 A 57 THR LYS SER ALA ARG GLY TYR ASP GLU ASP GLU VAL ASN SEQRES 3 A 57 GLU PHE LEU ALA GLN VAL ARG LYS ASP TYR GLU ILE VAL SEQRES 4 A 57 LEU ARG LYS LYS THR GLU LEU GLU ALA LYS VAL ASN GLU SEQRES 5 A 57 LEU ASP GLU ARG ILE SEQRES 1 B 57 MET PRO LEU THR PRO ASN ASP ILE HIS ASN LYS THR PHE SEQRES 2 B 57 THR LYS SER ALA ARG GLY TYR ASP GLU ASP GLU VAL ASN SEQRES 3 B 57 GLU PHE LEU ALA GLN VAL ARG LYS ASP TYR GLU ILE VAL SEQRES 4 B 57 LEU ARG LYS LYS THR GLU LEU GLU ALA LYS VAL ASN GLU SEQRES 5 B 57 LEU ASP GLU ARG ILE SEQRES 1 C 57 MET PRO LEU THR PRO ASN ASP ILE HIS ASN LYS THR PHE SEQRES 2 C 57 THR LYS SER ALA ARG GLY TYR ASP GLU ASP GLU VAL ASN SEQRES 3 C 57 GLU PHE LEU ALA GLN VAL ARG LYS ASP TYR GLU ILE VAL SEQRES 4 C 57 LEU ARG LYS LYS THR GLU LEU GLU ALA LYS VAL ASN GLU SEQRES 5 C 57 LEU ASP GLU ARG ILE SEQRES 1 D 57 MET PRO LEU THR PRO ASN ASP ILE HIS ASN LYS THR PHE SEQRES 2 D 57 THR LYS SER ALA ARG GLY TYR ASP GLU ASP GLU VAL ASN SEQRES 3 D 57 GLU PHE LEU ALA GLN VAL ARG LYS ASP TYR GLU ILE VAL SEQRES 4 D 57 LEU ARG LYS LYS THR GLU LEU GLU ALA LYS VAL ASN GLU SEQRES 5 D 57 LEU ASP GLU ARG ILE FORMUL 5 HOH *388(H2 O) HELIX 1 1 THR A 4 LYS A 11 1 8 HELIX 2 2 ASP A 21 ARG A 56 1 36 HELIX 3 3 THR B 4 LYS B 11 1 8 HELIX 4 4 ASP B 21 ASN B 51 1 31 HELIX 5 5 THR C 4 LYS C 11 1 8 HELIX 6 6 ASP C 21 GLU C 55 1 35 HELIX 7 7 THR D 4 LYS D 11 1 8 HELIX 8 8 ASP D 21 GLU D 52 1 32 SHEET 1 A 2 ARG A 18 TYR A 20 0 SHEET 2 A 2 LYS B 15 ALA B 17 -1 O SER B 16 N GLY A 19 SHEET 1 B 2 LYS C 15 TYR C 20 0 SHEET 2 B 2 LYS D 15 TYR D 20 -1 O GLY D 19 N SER C 16 CRYST1 57.682 28.566 66.179 90.00 105.92 90.00 P 1 21 1 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 0.017336 0.000000 0.004945 0.00000 SCALE2 0.000000 0.035007 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015713 0.00000 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 2 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 2 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 3 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 3 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 3 0.000000 0.000000 1.000000 0.00000 1