HEADER CELL ADHESION 27-MAR-23 8OK3 TITLE STRUCTURE OF THE C-TERMINAL DOMAIN OF THE BDELLOVIBRIO BACTERIOVORUS TITLE 2 BD2133 FIBRE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BD2133; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BDELLOVIBRIO BACTERIOVORUS HD100; SOURCE 3 ORGANISM_TAXID: 264462; SOURCE 4 GENE: BD2133; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS FIBRE, ADHESIN, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR S.G.CAULTON,A.L.LOVERING REVDAT 1 25-OCT-23 8OK3 0 JRNL AUTH S.G.CAULTON,A.L.LOVERING JRNL TITL STRUCTURE OF THE C-TERMINAL DOMAIN OF THE BDELLOVIBRIO JRNL TITL 2 BACTERIOVORUS BD2133 FIBRE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 17441 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.151 REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.159 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.750 REMARK 3 FREE R VALUE TEST SET COUNT : 828 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.730 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 13.3515 19.0648 1.8519 REMARK 3 T TENSOR REMARK 3 T11: 0.1128 T22: 0.1061 REMARK 3 T33: 0.1108 T12: -0.0033 REMARK 3 T13: 0.0046 T23: 0.0023 REMARK 3 L TENSOR REMARK 3 L11: 0.2941 L22: 0.2247 REMARK 3 L33: 0.5146 L12: -0.1958 REMARK 3 L13: -0.0779 L23: -0.1196 REMARK 3 S TENSOR REMARK 3 S11: 0.0167 S12: 0.0184 S13: 0.0348 REMARK 3 S21: -0.0359 S22: -0.0045 S23: -0.0327 REMARK 3 S31: -0.0833 S32: -0.0021 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 8OK3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1292129413. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-SEP-21 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 : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17441 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.03M MAGNESIUM CHLORIDE, 0.03M REMARK 280 CALCIUM CHLORIDE, 0.1 M IMIDAZOLE/MES PH 6.5, 12.5 % V/V MPD, REMARK 280 12.5 % PEG 1000, 12.5 % W/V PEG 3350, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 3 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 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 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 34.38000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.38000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.38000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.38000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.38000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.38000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 34.38000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 34.38000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 34.38000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 34.38000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 34.38000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 34.38000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 34.38000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 34.38000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 34.38000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 34.38000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 34.38000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 34.38000 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 S SO4 A1101 LIES ON A SPECIAL POSITION. REMARK 375 O2 SO4 A1101 LIES ON A SPECIAL POSITION. REMARK 375 NA NA A1102 LIES ON A SPECIAL POSITION. REMARK 375 CL CL A1104 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1201 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1202 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1212 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1317 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1330 LIES ON A SPECIAL POSITION. 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 907 REMARK 465 GLY A 908 REMARK 465 SER A 909 REMARK 465 ALA A 910 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1102 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 993 O REMARK 620 2 TYR A 993 O 0.0 REMARK 620 N 1 DBREF 8OK3 A 910 1031 UNP Q6ML84 Q6ML84_BDEBA 910 1031 SEQADV 8OK3 GLY A 907 UNP Q6ML84 EXPRESSION TAG SEQADV 8OK3 GLY A 908 UNP Q6ML84 EXPRESSION TAG SEQADV 8OK3 SER A 909 UNP Q6ML84 EXPRESSION TAG SEQRES 1 A 125 GLY GLY SER ALA ALA THR TRP THR SER LEU GLY LEU THR SEQRES 2 A 125 SER LEU GLY ALA VAL SER MET THR THR THR THR GLU GLN SEQRES 3 A 125 SER PHE THR LEU PRO VAL ALA ALA GLN THR ALA SER GLN SEQRES 4 A 125 ILE LEU VAL TYR LEU ARG CYS HIS SER GLY ASN ALA SER SEQRES 5 A 125 THR THR GLY ALA ASP ASP ILE ARG ILE TYR THR LYS GLU SEQRES 6 A 125 GLY ALA ALA THR TYR ASP HIS TYR LEU LEU MET PHE PRO SEQRES 7 A 125 TYR ALA GLY GLN GLY ALA VAL GLY TYR ASN SER ASP SER SEQRES 8 A 125 PHE TRP LEU PRO LYS THR SER ASP ASN LYS ILE TYR LEU SEQRES 9 A 125 ALA HIS SER MET ALA PRO GLY SER ALA ASN SER GLY CYS SEQRES 10 A 125 ASN PHE TYR ILE THR GLY TYR LYS HET SO4 A1101 5 HET NA A1102 1 HET CL A1103 1 HET CL A1104 1 HETNAM SO4 SULFATE ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 NA NA 1+ FORMUL 4 CL 2(CL 1-) FORMUL 6 HOH *130(H2 O) HELIX 1 AA1 PRO A 937 ALA A 943 5 7 SHEET 1 AA1 4 THR A 914 ALA A 923 0 SHEET 2 AA1 4 SER A1021 LYS A1031 -1 O TYR A1030 N THR A 914 SHEET 3 AA1 4 GLN A 945 SER A 954 -1 N LEU A 947 O GLY A1029 SHEET 4 AA1 4 GLY A 992 PRO A1001 -1 O GLY A 992 N SER A 954 SHEET 1 AA2 4 GLN A 932 THR A 935 0 SHEET 2 AA2 4 LYS A1007 ALA A1011 -1 O LEU A1010 N GLN A 932 SHEET 3 AA2 4 ASP A 963 GLU A 971 -1 N ARG A 966 O ALA A1011 SHEET 4 AA2 4 ALA A 974 MET A 982 -1 O LEU A 980 N ILE A 965 SHEET 1 AA3 2 ASN A 956 ALA A 957 0 SHEET 2 AA3 2 TYR A 985 ALA A 986 1 N TYR A 985 O ALA A 957 LINK O TYR A 993 NA NA A1102 1555 1555 2.16 LINK O TYR A 993 NA NA A1102 1555 5555 2.16 CRYST1 68.760 68.760 68.760 90.00 90.00 90.00 P 21 3 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 0.014543 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014543 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014543 0.00000