HEADER UNKNOWN FUNCTION 26-APR-21 7OC9 TITLE STRUCTURE OF BDELLOVIBRIO BACTERIOVORUS BD0675 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BD0675; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BDELLOVIBRIO BACTERIOVORUS (STRAIN ATCC 15356 / SOURCE 3 DSM 50701 / NCIB 9529 / HD100); SOURCE 4 ORGANISM_TAXID: 264462; SOURCE 5 STRAIN: ATCC 15356 / DSM 50701 / NCIB 9529 / HD100; SOURCE 6 GENE: BD0675; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS BDELLOVIBRIO SECRETION CRYPTIC, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR A.L.LOVERING,M.VALDIVIA-DELGADO REVDAT 3 08-DEC-21 7OC9 1 JRNL REMARK REVDAT 2 03-NOV-21 7OC9 1 JRNL REMARK REVDAT 1 05-MAY-21 7OC9 0 JRNL AUTH L.T.ALEXANDER,R.LEPORE,A.KRYSHTAFOVYCH,A.ADAMOPOULOS, JRNL AUTH 2 M.ALAHUHTA,A.M.ARVIN,Y.J.BOMBLE,B.BOTTCHER,C.BREYTON, JRNL AUTH 3 V.CHIARINI,N.B.CHINNAM,W.CHIU,K.FIDELIS,R.GRINTER,G.D.GUPTA, JRNL AUTH 4 M.D.HARTMANN,C.S.HAYES,T.HEIDEBRECHT,A.ILARI,A.JOACHIMIAK, JRNL AUTH 5 Y.KIM,R.LINARES,A.L.LOVERING,V.V.LUNIN,A.N.LUPAS,C.MAKBUL, JRNL AUTH 6 K.MICHALSKA,J.MOULT,P.K.MUKHERJEE,W.S.NUTT,S.L.OLIVER, JRNL AUTH 7 A.PERRAKIS,L.STOLS,J.A.TAINER,M.TOPF,S.E.TSUTAKAWA, JRNL AUTH 8 M.VALDIVIA-DELGADO,T.SCHWEDE JRNL TITL TARGET HIGHLIGHTS IN CASP14: ANALYSIS OF MODELS BY STRUCTURE JRNL TITL 2 PROVIDERS. JRNL REF PROTEINS V. 89 1647 2021 JRNL REFN ESSN 1097-0134 JRNL PMID 34561912 JRNL DOI 10.1002/PROT.26247 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 42.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 25800 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 1260 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 42.4280 - 3.1199 1.00 2896 137 0.1775 0.1814 REMARK 3 2 3.1199 - 2.4764 1.00 2798 131 0.2170 0.2411 REMARK 3 3 2.4764 - 2.1634 1.00 2722 163 0.2095 0.2386 REMARK 3 4 2.1634 - 1.9656 0.99 2726 121 0.2076 0.2428 REMARK 3 5 1.9656 - 1.8247 0.99 2712 123 0.2178 0.2507 REMARK 3 6 1.8247 - 1.7171 0.99 2705 145 0.2219 0.2312 REMARK 3 7 1.7171 - 1.6311 0.99 2634 170 0.2341 0.2892 REMARK 3 8 1.6311 - 1.5601 0.98 2674 134 0.2634 0.2468 REMARK 3 9 1.5601 - 1.5001 0.98 2673 136 0.3021 0.3421 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.44 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 : 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 7OC9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-APR-21. REMARK 100 THE DEPOSITION ID IS D_1292115464. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 0.9119 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25800 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 42.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.04177 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.2700 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) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.88700 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: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 47% V/V MPD 2% T-BUTANOL, PH 7.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.92500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.92500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 26.74500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.83500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 26.74500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.83500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 42.92500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 26.74500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 34.83500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 42.92500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 26.74500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 34.83500 REMARK 290 SMTRY3 8 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 9.0 KCAL/MOL 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 HOH A 372 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 1 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 A 34 NE2 GLN A 36 1.91 REMARK 500 N GLY A 2 O HOH A 301 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 PRO A 85 108.67 -59.71 REMARK 500 ASP A 88 -158.22 -156.32 REMARK 500 PHE A 93 -1.99 72.52 REMARK 500 MET A 120 24.17 -68.26 REMARK 500 ASP A 121 45.95 -151.32 REMARK 500 REMARK 500 REMARK: NULL DBREF 7OC9 A 1 134 UNP Q6MQ12 Q6MQ12_BDEBA 69 202 SEQRES 1 A 134 GLY GLY ASN ASP PHE VAL SER ARG LEU LYS ALA LEU ASP SEQRES 2 A 134 GLY ARG GLU GLY LYS ILE VAL SER SER TYR ASP ASP GLU SEQRES 3 A 134 ASN THR GLY ARG CYS ARG LEU GLU LEU GLN LYS TYR GLU SEQRES 4 A 134 LEU GLU ASP GLY SER GLN GLY LEU ALA VAL TYR LEU GLN SEQRES 5 A 134 ASP THR GLY MET TYR PHE THR PRO SER ALA GLY LEU ASP SEQRES 6 A 134 LYS GLU THR LYS LEU LYS ASP ALA ASN THR ALA VAL VAL SEQRES 7 A 134 SER THR SER SER GLU ARG PRO GLY GLY ASP ALA CYS GLY SEQRES 8 A 134 ASP PHE GLY GLY ALA LEU GLY TYR LYS LYS VAL LEU VAL SEQRES 9 A 134 LEU LYS ASP ASN GLN VAL THR ILE ARG GLU THR PHE ARG SEQRES 10 A 134 CYS VAL MET ASP GLY PHE LYS LYS TYR ASP LEU SER THR SEQRES 11 A 134 THR CYS GLN PHE HET MPD A 201 22 HET GOL A 202 14 HET TBU A 203 15 HET TBU A 204 15 HET TBU A 205 15 HET TBU A 206 15 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM GOL GLYCEROL HETNAM TBU TERTIARY-BUTYL ALCOHOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN TBU 2-METHYL-2-PROPANOL FORMUL 2 MPD C6 H14 O2 FORMUL 3 GOL C3 H8 O3 FORMUL 4 TBU 4(C4 H10 O) FORMUL 8 HOH *74(H2 O) HELIX 1 AA1 GLY A 2 ASP A 13 1 12 HELIX 2 AA2 MET A 120 GLY A 122 5 3 SHEET 1 AA1 9 SER A 61 LEU A 64 0 SHEET 2 AA1 9 GLN A 45 GLN A 52 -1 N LEU A 47 O LEU A 64 SHEET 3 AA1 9 ARG A 30 GLU A 39 -1 N ARG A 32 O GLN A 52 SHEET 4 AA1 9 GLU A 16 SER A 22 -1 N GLY A 17 O CYS A 31 SHEET 5 AA1 9 LYS A 125 GLN A 133 -1 O GLN A 133 N LYS A 18 SHEET 6 AA1 9 GLN A 109 CYS A 118 -1 N PHE A 116 O TYR A 126 SHEET 7 AA1 9 ALA A 96 LYS A 106 -1 N VAL A 104 O THR A 111 SHEET 8 AA1 9 THR A 75 SER A 79 -1 N ALA A 76 O LEU A 103 SHEET 9 AA1 9 LYS A 69 ASP A 72 -1 N LYS A 69 O VAL A 77 SHEET 1 AA2 2 GLY A 87 ASP A 88 0 SHEET 2 AA2 2 GLY A 91 ASP A 92 -1 O GLY A 91 N ASP A 88 SSBOND 1 CYS A 31 CYS A 132 1555 1555 2.01 SSBOND 2 CYS A 90 CYS A 118 1555 1555 2.03 CRYST1 53.490 69.670 85.850 90.00 90.00 90.00 C 2 2 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 0.018695 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014353 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011648 0.00000