HEADER HYDROLASE 12-MAY-19 6K1T TITLE THE STRUCTURE OF FRANCISELLA VIRULENCE FACTOR BIOJ COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA/BETA HYDROLASE FOLD FAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FRANCISELLA PHILOMIRAGIA SUBSP. PHILOMIRAGIA SOURCE 3 ATCC 25015; SOURCE 4 ORGANISM_TAXID: 539329; SOURCE 5 GENE: BZ13_192; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS VIRULENCE FACTOR BIOJ, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.OUYANG,H.GUAN,S.ZHANG REVDAT 2 06-MAR-24 6K1T 1 REMARK REVDAT 1 15-APR-20 6K1T 0 JRNL AUTH W.WEI,H.GUAN,T.ZHU,S.ZHANG,C.FAN,S.OUYANG,Y.FENG JRNL TITL MOLECULAR BASIS OF BIOJ, A UNIQUE GATEKEEPER IN BACTERIAL JRNL TITL 2 BIOTIN SYNTHESIS. JRNL REF ISCIENCE V. 19 796 2019 JRNL REFN ESSN 2589-0042 JRNL PMID 31494495 JRNL DOI 10.1016/J.ISCI.2019.08.028 REMARK 2 REMARK 2 RESOLUTION. 1.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 3 NUMBER OF REFLECTIONS : 37007 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 1808 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 40.2205 - 3.7232 0.89 2697 156 0.1820 0.2059 REMARK 3 2 3.7232 - 2.9555 0.95 2832 158 0.1918 0.2151 REMARK 3 3 2.9555 - 2.5819 0.98 2924 163 0.2071 0.2293 REMARK 3 4 2.5819 - 2.3459 0.96 2839 172 0.2098 0.2180 REMARK 3 5 2.3459 - 2.1778 0.96 2854 131 0.1991 0.2667 REMARK 3 6 2.1778 - 2.0494 0.94 2811 150 0.2068 0.2318 REMARK 3 7 2.0494 - 1.9468 0.93 2770 121 0.2114 0.2686 REMARK 3 8 1.9468 - 1.8620 0.85 1742 88 0.2635 0.3412 REMARK 3 9 1.8620 - 1.7903 0.90 2662 142 0.2398 0.2858 REMARK 3 10 1.7903 - 1.7285 0.90 2691 119 0.2458 0.2730 REMARK 3 11 1.7285 - 1.6745 0.93 2767 137 0.2427 0.2628 REMARK 3 12 1.6745 - 1.6266 0.94 2778 138 0.2475 0.3007 REMARK 3 13 1.6266 - 1.5838 0.95 2832 133 0.2590 0.2741 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.410 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 2505 REMARK 3 ANGLE : 0.808 3394 REMARK 3 CHIRALITY : 0.051 368 REMARK 3 PLANARITY : 0.005 432 REMARK 3 DIHEDRAL : 2.726 1503 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 6K1T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1300012163. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-18 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 : SSRF REMARK 200 BEAMLINE : BL17U 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37190 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 51.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.67 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL 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: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD 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 (%): 42.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (V/V) PEG 6000, 100MM REMARK 280 BICINE/SODIUM HYDROXIDE (PH 9.0), COUNTER-DIFFUSION, TEMPERATURE REMARK 280 289.15K 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 33.65650 REMARK 290 SMTRY3 2 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 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 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 GLU A 213 REMARK 465 ASP A 214 REMARK 465 ILE A 215 REMARK 465 MET A 216 REMARK 465 SER A 217 REMARK 465 GLU A 218 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 OE2 GLU A 204 O HOH A 401 2.06 REMARK 500 OD2 ASP A 239 NH1 ARG A 306 2.10 REMARK 500 OH TYR A 176 O HOH A 402 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 A 57 -0.16 75.13 REMARK 500 SER A 84 176.13 72.77 REMARK 500 SER A 151 -114.56 55.52 REMARK 500 TYR A 176 64.83 27.21 REMARK 500 HIS A 197 -63.59 74.02 REMARK 500 LYS A 221 31.66 -74.59 REMARK 500 REMARK 500 REMARK: NULL DBREF 6K1T A 1 306 UNP C6YW90 C6YW90_9GAMM 1 306 SEQADV 6K1T ASN A 236 UNP C6YW90 LYS 236 CONFLICT SEQRES 1 A 306 MET PRO TYR HIS PRO ALA LEU GLU SER LEU LEU ASP THR SEQRES 2 A 306 PRO GLU ILE ARG LYS ILE LYS LYS LEU ASP LEU ARG ASP SEQRES 3 A 306 GLN ARG LYS ILE PHE ALA ASP LEU SER ILE ALA GLN ILE SEQRES 4 A 306 LYS ARG LEU PRO ARG PRO ASP ILE ILE GLU GLU ASP ILE SEQRES 5 A 306 LYS LEU GLU ASN ASP THR ILE LEU ARG HIS TYR LYS PRO SEQRES 6 A 306 LYS LYS ALA SER ASP LYS ALA VAL LEU PHE ILE HIS GLY SEQRES 7 A 306 GLY GLY TRP CYS LEU SER SER ILE ASP THR TYR ASP HIS SEQRES 8 A 306 VAL CYS ARG TYR LEU CYS ASP GLN GLY ASN LEU ASN ILE SEQRES 9 A 306 PHE SER LEU GLU TYR GLY LEU GLY PRO GLU ASP LYS TYR SEQRES 10 A 306 PRO ALA ALA VAL ASN HIS ALA LEU TYR ALA TYR ASP TRP SEQRES 11 A 306 LEU TYR GLU ASN ILE THR LYS PHE ASN LEU SER THR GLU SEQRES 12 A 306 ASN ILE PHE VAL MET GLY ASP SER ALA GLY GLY ASN LEU SEQRES 13 A 306 VAL THR ILE ILE CYS HIS GLU ARG GLN GLU ASN MET PRO SEQRES 14 A 306 LYS ALA GLN ILE LEU VAL TYR PRO ALA VAL ASP MET TYR SEQRES 15 A 306 THR LYS TYR ASP SER ASN THR LYS PHE ASP GLU TYR LYS SEQRES 16 A 306 TYR HIS LEU THR THR GLU TRP CYS GLU LEU PHE LEU LYS SEQRES 17 A 306 ALA TYR ILE GLY GLU ASP ILE MET SER GLU PRO LYS LYS SEQRES 18 A 306 LEU ARG GLN PRO THR ILE SER PRO LEU PHE TYR LYS ASP SEQRES 19 A 306 THR ASN GLN PRO ASP THR LEU ILE VAL ALA ALA THR HIS SEQRES 20 A 306 ASP ILE LEU ILE ASP GLY ILE TYR ALA TYR GLU GLU LYS SEQRES 21 A 306 LEU LYS GLN GLN GLY THR TYR VAL GLU THR HIS TYR ASP SEQRES 22 A 306 ASP GLU MET TYR HIS GLY PHE ILE GLY GLY LEU GLY VAL SEQRES 23 A 306 VAL PRO PHE GLU ASN PRO LYS ILE ALA LEU ASP LYS ILE SEQRES 24 A 306 ILE GLU PHE ILE ASN LYS ARG FORMUL 2 HOH *216(H2 O) HELIX 1 AA1 ALA A 6 ASP A 12 1 7 HELIX 2 AA2 THR A 13 LYS A 21 1 9 HELIX 3 AA3 ASP A 23 ARG A 41 1 19 HELIX 4 AA4 SER A 85 THR A 88 5 4 HELIX 5 AA5 TYR A 89 ASN A 101 1 13 HELIX 6 AA6 PRO A 118 ILE A 135 1 18 HELIX 7 AA7 THR A 136 ASN A 139 5 4 HELIX 8 AA8 SER A 141 GLU A 143 5 3 HELIX 9 AA9 SER A 151 ARG A 164 1 14 HELIX 10 AB1 GLN A 165 MET A 168 5 4 HELIX 11 AB2 ASP A 186 PHE A 191 1 6 HELIX 12 AB3 GLU A 193 HIS A 197 5 5 HELIX 13 AB4 THR A 199 ILE A 211 1 13 HELIX 14 AB5 PRO A 219 ARG A 223 5 5 HELIX 15 AB6 SER A 228 TYR A 232 5 5 HELIX 16 AB7 LEU A 250 GLN A 264 1 15 HELIX 17 AB8 GLY A 279 LEU A 284 5 6 HELIX 18 AB9 GLU A 290 LYS A 305 1 16 SHEET 1 AA1 8 ILE A 48 LYS A 53 0 SHEET 2 AA1 8 ILE A 59 LYS A 64 -1 O HIS A 62 N GLU A 50 SHEET 3 AA1 8 ASN A 103 GLU A 108 -1 O ILE A 104 N TYR A 63 SHEET 4 AA1 8 ALA A 72 ILE A 76 1 N VAL A 73 O PHE A 105 SHEET 5 AA1 8 ILE A 145 ASP A 150 1 O PHE A 146 N LEU A 74 SHEET 6 AA1 8 ALA A 171 VAL A 175 1 O VAL A 175 N GLY A 149 SHEET 7 AA1 8 ASP A 239 HIS A 247 1 O LEU A 241 N LEU A 174 SHEET 8 AA1 8 VAL A 268 TYR A 277 1 O ASP A 273 N ALA A 244 CISPEP 1 GLY A 112 PRO A 113 0 3.02 CISPEP 2 TYR A 117 PRO A 118 0 9.46 CRYST1 43.943 67.313 55.571 90.00 112.55 90.00 P 1 21 1 2 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 0.022757 0.000000 0.009450 0.00000 SCALE2 0.000000 0.014856 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019485 0.00000