HEADER HYDROLASE 30-JUN-19 6KD0 TITLE CRYSTAL STRUCTURE OF VIBRALACTONE CYCLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: VIBRALACTONE CYCLASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOREOSTEREUM VIBRANS; SOURCE 3 ORGANISM_TAXID: 1826779; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS VIBRALACTONE CYCLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZENG,K.N.FENG REVDAT 2 22-NOV-23 6KD0 1 REMARK REVDAT 1 24-JUN-20 6KD0 0 JRNL AUTH K.N.FENG,Y.L.YANG,Y.X.XU,Y.ZHANG,T.FENG,S.X.HUANG,J.K.LIU, JRNL AUTH 2 Y.ZENG JRNL TITL A HYDROLASE-CATALYZED CYCLIZATION FORMS THE FUSED BICYCLIC JRNL TITL 2 BETA-LACTONE IN VIBRALACTONE. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 59 7209 2020 JRNL REFN ESSN 1521-3773 JRNL PMID 32050043 JRNL DOI 10.1002/ANIE.202000710 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 37766 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 2019 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.84 REMARK 3 REFLECTION IN BIN (WORKING SET) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.1700 REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : 0.2000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2728 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 268 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6KD0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1300012756. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAY-19 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 : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.988 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39851 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.63100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 5LK6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K 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 40.11700 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 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 ALA A 2 -164.12 -103.76 REMARK 500 LEU A 7 -87.19 -96.68 REMARK 500 GLU A 9 43.62 140.75 REMARK 500 VAL A 45 -57.04 -121.66 REMARK 500 TRP A 106 -9.69 73.99 REMARK 500 PRO A 143 35.83 -98.49 REMARK 500 SER A 177 -122.08 56.75 REMARK 500 TYR A 208 57.35 36.87 REMARK 500 LEU A 236 -16.97 72.52 REMARK 500 TRP A 280 73.48 -101.39 REMARK 500 REMARK 500 REMARK: NULL DBREF 6KD0 A 1 343 PDB 6KD0 6KD0 1 343 SEQRES 1 A 343 MET ALA ILE THR LEU PHE LEU ASP GLU GLY LEU SER THR SEQRES 2 A 343 ALA HIS PRO GLU PHE ALA PRO VAL TRP ALA ALA PHE PRO SEQRES 3 A 343 GLN PRO THR ASP PRO PHE PRO PRO LEU GLU ALA ARG ARG SEQRES 4 A 343 ALA PHE TRP ASP GLU VAL VAL ILE PRO ASN LEU ASN LYS SEQRES 5 A 343 PHE LEU GLU PRO SER LEU PRO SER GLU ASP ARG TYR ARG SEQRES 6 A 343 LEU GLU ASP TYR TYR ILE PRO VAL GLU GLY THR ASN MET SEQRES 7 A 343 HIS VAL ARG THR TYR ILE PRO THR SER SER PRO ASP LYS SEQRES 8 A 343 THR LYS THR TYR PRO LEU LEU TYR TRP VAL HIS CYS GLY SEQRES 9 A 343 GLY TRP ALA ILE GLY ASN TYR GLU MET ASP ASP TYR ASP SEQRES 10 A 343 LEU ARG ILE ILE CYS ASP LYS LEU GLN VAL CYS ALA VAL SEQRES 11 A 343 SER ILE ASP TYR ARG LEU THR PRO GLU SER SER SER PRO SEQRES 12 A 343 THR GLY ALA LYS ASP VAL TYR ALA GLY LEU LYS TRP ALA SEQRES 13 A 343 ALA ALA ASN ALA GLY SER PHE ASN ALA ASP PRO LYS LYS SEQRES 14 A 343 GLY PHE VAL ILE ALA GLY GLN SER ALA GLY GLY ASN LEU SEQRES 15 A 343 SER LEU ILE ALA ALA HIS TRP ALA ARG ASP ASP PRO PHE SEQRES 16 A 343 PHE ALA ASN THR PRO LEU THR GLY GLN LEU VAL GLN TYR SEQRES 17 A 343 PRO PRO THR CYS HIS PRO GLU ALA MET PRO GLU GLU TYR SEQRES 18 A 343 LYS SER CYS ILE LYS SER MET GLU GLU CYS ARG ASP ALA SEQRES 19 A 343 PRO LEU LEU SER LYS LYS GLU VAL TYR TRP PHE ASN GLU SEQRES 20 A 343 LEU ALA ASN PRO ALA ASP PRO HIS ASP PRO SER PHE SER SEQRES 21 A 343 PRO LEU LEU PHE PRO SER HIS ALA ASN LEU PRO PRO LEU SEQRES 22 A 343 PHE PHE MET SER CYS GLY TRP ASP PRO LEU ARG ASP GLU SEQRES 23 A 343 GLY LEU LEU TYR HIS ALA LEU VAL LYS GLU ALA GLY VAL SEQRES 24 A 343 GLU THR ARG MET THR MET TYR PRO GLY VAL PRO HIS ALA SEQRES 25 A 343 PHE HIS MET LEU PHE ARG SER MET LYS LEU ALA GLN LYS SEQRES 26 A 343 PHE GLN GLU GLU THR ILE GLU GLY MET SER TRP LEU PHE SEQRES 27 A 343 SER LYS THR PRO GLN FORMUL 2 HOH *268(H2 O) HELIX 1 AA1 GLU A 17 PHE A 25 1 9 HELIX 2 AA2 PRO A 34 VAL A 45 1 12 HELIX 3 AA3 VAL A 45 GLU A 55 1 11 HELIX 4 AA4 PRO A 56 LEU A 58 5 3 HELIX 5 AA5 SER A 60 ASP A 62 5 3 HELIX 6 AA6 ASN A 110 MET A 113 5 4 HELIX 7 AA7 ASP A 114 GLN A 126 1 13 HELIX 8 AA8 PRO A 143 ASN A 159 1 17 HELIX 9 AA9 ALA A 160 ASN A 164 5 5 HELIX 10 AB1 ASP A 166 LYS A 169 5 4 HELIX 11 AB2 SER A 177 ASP A 193 1 17 HELIX 12 AB3 PRO A 194 ALA A 197 5 4 HELIX 13 AB4 HIS A 213 MET A 217 5 5 HELIX 14 AB5 PRO A 218 ILE A 225 5 8 HELIX 15 AB6 LYS A 226 CYS A 231 1 6 HELIX 16 AB7 SER A 238 ASN A 250 1 13 HELIX 17 AB8 SER A 260 PHE A 264 5 5 HELIX 18 AB9 LEU A 283 ALA A 297 1 15 HELIX 19 AC1 ALA A 312 PHE A 317 1 6 HELIX 20 AC2 MET A 320 SER A 339 1 20 SHEET 1 AA1 8 TYR A 64 VAL A 73 0 SHEET 2 AA1 8 THR A 76 PRO A 85 -1 O THR A 76 N VAL A 73 SHEET 3 AA1 8 CYS A 128 ILE A 132 -1 O SER A 131 N ARG A 81 SHEET 4 AA1 8 LEU A 97 VAL A 101 1 N TRP A 100 O VAL A 130 SHEET 5 AA1 8 PHE A 171 GLN A 176 1 O VAL A 172 N TYR A 99 SHEET 6 AA1 8 GLY A 203 GLN A 207 1 O LEU A 205 N ILE A 173 SHEET 7 AA1 8 LEU A 273 TRP A 280 1 O PHE A 274 N GLN A 204 SHEET 8 AA1 8 THR A 301 PRO A 310 1 O TYR A 306 N GLY A 279 CISPEP 1 THR A 137 PRO A 138 0 -6.13 CISPEP 2 SER A 142 PRO A 143 0 9.01 CRYST1 47.324 80.234 59.184 90.00 102.36 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 0.021131 0.000000 0.004630 0.00000 SCALE2 0.000000 0.012464 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017297 0.00000