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- PDB-6a98: Crystal structure of a cyclase from Fischerella sp. TAU -

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Basic information

Entry
Database: PDB / ID: 6a98
TitleCrystal structure of a cyclase from Fischerella sp. TAU
Componentsaromatic prenyltransferase
KeywordsTRANSFERASE / prenyltransferase
Function / homologyFisC
Function and homology information
Biological speciesFischerella ambigua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsHu, X.Y. / Liu, W.D. / Chen, C.C. / Guo, R.T.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: The Crystal Structure of a Class of Cyclases that Catalyze the Cope Rearrangement
Authors: Chen, C.C. / Hu, X. / Tang, X. / Yang, Y. / Ko, T.P. / Gao, J. / Zheng, Y. / Huang, J.W. / Yu, Z. / Li, L. / Han, S. / Cai, N. / Zhang, Y. / Liu, W. / Guo, R.T.
History
DepositionJul 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: aromatic prenyltransferase
B: aromatic prenyltransferase
C: aromatic prenyltransferase
D: aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,20214
Polymers96,4674
Non-polymers73510
Water12,052669
1
A: aromatic prenyltransferase
C: aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6867
Polymers48,2342
Non-polymers4535
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-27 kcal/mol
Surface area17070 Å2
MethodPISA
2
B: aromatic prenyltransferase
D: aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5167
Polymers48,2342
Non-polymers2825
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-26 kcal/mol
Surface area17190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.442, 53.340, 95.162
Angle α, β, γ (deg.)104.54, 91.39, 92.91
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
aromatic prenyltransferase


Mass: 24116.777 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fischerella ambigua (bacteria) / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1P8VSL7
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 669 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.67 % / Mosaicity: 0.799 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1.0M sodium citrate, 0.1M Imidazole pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 19, 2018
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→25 Å / Num. obs: 64099 / % possible obs: 97.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.028 / Rrim(I) all: 0.053 / Χ2: 1.597 / Net I/σ(I): 18.1 / Num. measured all: 215791
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.82-1.943.50.25158740.9640.1570.2971.41395.4
1.94-2.013.60.20359340.9740.1260.2391.46296.4
2.01-2.113.60.1559760.9850.0930.1761.52196.7
2.11-2.223.60.1260480.9880.0740.1411.52697
2.22-2.363.60.159650.9920.0620.1181.56397.3
2.36-2.543.60.0860270.9940.0490.0941.58497.6
2.54-2.793.60.0660570.9960.0370.071.63697.9
2.79-3.23.60.04160640.9980.0250.0481.70998.2
3.2-4.023.60.0360930.9990.0180.0351.75798.7
4.02-253.60.02561090.9990.0150.0291.78599

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YVK

5yvk


Resolution: 1.82→24.96 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.567 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20108 3324 5.2 %RANDOM
Rwork0.16503 ---
obs0.16688 60772 95.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.552 Å2
Baniso -1Baniso -2Baniso -3
1-3.54 Å2-0.38 Å20.6 Å2
2---0.83 Å2-0.15 Å2
3----2.31 Å2
Refinement stepCycle: 1 / Resolution: 1.82→24.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6132 0 36 669 6837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0146365
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175599
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.6718614
X-RAY DIFFRACTIONr_angle_other_deg0.9221.64313131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1215797
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.81323.808302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.0415938
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5791524
X-RAY DIFFRACTIONr_chiral_restr0.0740.2848
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027131
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021149
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6873.0883232
X-RAY DIFFRACTIONr_mcbond_other2.6883.0873230
X-RAY DIFFRACTIONr_mcangle_it3.7854.6143995
X-RAY DIFFRACTIONr_mcangle_other3.7844.6153996
X-RAY DIFFRACTIONr_scbond_it3.4053.4863133
X-RAY DIFFRACTIONr_scbond_other3.4053.4863134
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0975.0874620
X-RAY DIFFRACTIONr_long_range_B_refined7.74262.0531605
X-RAY DIFFRACTIONr_long_range_B_other7.73461.99831506
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.821→1.868 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 175 -
Rwork0.269 3420 -
obs--72.67 %

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