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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 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
TER 2444 ARG A 306
MASTER 241 0 0 18 8 0 0 6 2659 1 0 24
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