HEADER PROTEIN BINDING 01-APR-21 7O39 TITLE CRYSTAL STRUCTURE OF S. AUREUS DIVIVA N TERMINAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIVIVA; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS (STRAIN NCTC 8325 / PS SOURCE 3 47); SOURCE 4 ORGANISM_TAXID: 93061; SOURCE 5 STRAIN: NCTC 8325 / PS 47; SOURCE 6 GENE: SAOUHSC_01158; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: POPINRSF KEYWDS CELL DIVISION, DIVISOME, MOLECULAR RULER, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR V.A.RAO,S.BOOTH,R.J.LEWIS REVDAT 2 31-JAN-24 7O39 1 REMARK REVDAT 1 14-APR-21 7O39 0 JRNL AUTH V.A.RAO,S.BOOTH,R.J.LEWIS JRNL TITL CRYSTAL STRUCTURE OF S. AUREUS DIVIVA N TERMINAL DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 31123 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.840 REMARK 3 FREE R VALUE TEST SET COUNT : 1506 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 36.9500 - 2.8900 1.00 2913 131 0.1838 0.1860 REMARK 3 2 2.8900 - 2.2900 1.00 2748 128 0.1615 0.2005 REMARK 3 3 2.2900 - 2.0000 1.00 2715 135 0.1382 0.1834 REMARK 3 4 2.0000 - 1.8200 1.00 2710 139 0.1435 0.1799 REMARK 3 5 1.8200 - 1.6900 1.00 2700 119 0.1426 0.1672 REMARK 3 6 1.6900 - 1.5900 1.00 2653 143 0.1309 0.1612 REMARK 3 7 1.5900 - 1.5100 1.00 2643 142 0.1378 0.1938 REMARK 3 8 1.5100 - 1.4500 0.99 2617 161 0.1383 0.1738 REMARK 3 9 1.4500 - 1.3900 1.00 2615 147 0.1541 0.1734 REMARK 3 10 1.3900 - 1.3400 1.00 2636 131 0.1576 0.1985 REMARK 3 11 1.3400 - 1.3000 1.00 2667 130 0.1793 0.2012 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) : 0.118 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.228 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.87 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.98 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 : 0.006 835 REMARK 3 ANGLE : 0.747 1121 REMARK 3 CHIRALITY : 0.060 131 REMARK 3 PLANARITY : 0.007 147 REMARK 3 DIHEDRAL : 3.464 105 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 7O39 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-APR-21. REMARK 100 THE DEPOSITION ID IS D_1292115046. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-FEB-18 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 : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97623 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.6.2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31216 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 37.080 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.55600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.7.17 REMARK 200 STARTING MODEL: 2WUJ REMARK 200 REMARK 200 REMARK: CUBIC REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CARBOXYLIC ACIDS, 0.1 M BUFFER REMARK 280 SYSTEM 1 PH 6.5, 37.5 % V/V MPD_P1K_P3350; MORPHEUS G4, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 14.05400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.62450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.58750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.62450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.05400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.58750 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 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 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 A 1 REMARK 465 PRO A 2 REMARK 465 PRO A 3 REMARK 465 ASP A 55 REMARK 465 THR A 56 REMARK 465 ASN A 57 REMARK 465 ILE A 58 REMARK 465 LYS A 59 REMARK 465 GLY B 1 REMARK 465 PRO B 2 REMARK 465 PRO B 3 REMARK 465 ASP B 55 REMARK 465 THR B 56 REMARK 465 ASN B 57 REMARK 465 ILE B 58 REMARK 465 LYS B 59 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 18 CE NZ REMARK 470 GLU A 36 CD OE1 OE2 REMARK 470 LYS A 49 CD CE NZ REMARK 470 GLU A 52 CG CD OE1 OE2 REMARK 470 LYS B 10 CD CE NZ REMARK 470 GLU B 38 CG CD OE1 OE2 REMARK 470 LYS B 45 CD CE NZ REMARK 470 GLU B 52 CG CD OE1 OE2 REMARK 470 ARG B 54 CG CD NE CZ NH1 NH2 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 OE1 GLU B 22 OG1 THR B 24 2.08 REMARK 500 REMARK 500 REMARK: NULL DBREF 7O39 A 3 59 UNP Q2FZ83 Q2FZ83_STAA8 2 58 DBREF 7O39 B 3 59 UNP Q2FZ83 Q2FZ83_STAA8 2 58 SEQADV 7O39 GLY A 1 UNP Q2FZ83 EXPRESSION TAG SEQADV 7O39 PRO A 2 UNP Q2FZ83 EXPRESSION TAG SEQADV 7O39 GLY B 1 UNP Q2FZ83 EXPRESSION TAG SEQADV 7O39 PRO B 2 UNP Q2FZ83 EXPRESSION TAG SEQRES 1 A 59 GLY PRO PRO PHE THR PRO ASN GLU ILE LYS ASN LYS GLU SEQRES 2 A 59 PHE SER ARG VAL LYS ASN GLY LEU GLU PRO THR GLU VAL SEQRES 3 A 59 ALA ASN PHE LEU GLU GLN LEU SER THR GLU ILE GLU ARG SEQRES 4 A 59 LEU LYS GLU ASP LYS LYS GLN LEU GLU LYS VAL ILE GLU SEQRES 5 A 59 GLU ARG ASP THR ASN ILE LYS SEQRES 1 B 59 GLY PRO PRO PHE THR PRO ASN GLU ILE LYS ASN LYS GLU SEQRES 2 B 59 PHE SER ARG VAL LYS ASN GLY LEU GLU PRO THR GLU VAL SEQRES 3 B 59 ALA ASN PHE LEU GLU GLN LEU SER THR GLU ILE GLU ARG SEQRES 4 B 59 LEU LYS GLU ASP LYS LYS GLN LEU GLU LYS VAL ILE GLU SEQRES 5 B 59 GLU ARG ASP THR ASN ILE LYS FORMUL 3 HOH *172(H2 O) HELIX 1 AA1 THR A 5 LYS A 12 1 8 HELIX 2 AA2 GLU A 22 ARG A 54 1 33 HELIX 3 AA3 THR B 5 ASN B 11 1 7 HELIX 4 AA4 GLU B 22 ARG B 54 1 33 SHEET 1 AA1 2 ARG A 16 LEU A 21 0 SHEET 2 AA1 2 ARG B 16 LEU B 21 -1 O VAL B 17 N GLY A 20 CRYST1 28.108 39.175 111.249 90.00 90.00 90.00 P 21 21 21 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 0.035577 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025526 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008989 0.00000