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- PDB-5wqi: Structure of fungal meroterpenoid isomerase Trt14 complexed with ... -

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Basic information

Entry
Database: PDB / ID: 5wqi
TitleStructure of fungal meroterpenoid isomerase Trt14 complexed with hydrolyzed product
ComponentsIsomerase trt14
KeywordsISOMERASE / meroterpenoid / terretonin
Function / homology: / Isomerases / terpenoid biosynthetic process / isomerase activity / Chem-7X0 / Isomerase trt14
Function and homology information
Biological speciesAspergillus terreus NIH 2624 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 Å
AuthorsMori, T. / Matsuda, Y. / Abe, I.
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Molecular basis for the unusual ring reconstruction in fungal meroterpenoid biogenesis
Authors: Mori, T. / Iwabuchi, T. / Hoshino, S. / Wang, H. / Matsuda, Y. / Abe, I.
History
DepositionNov 27, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isomerase trt14
B: Isomerase trt14
C: Isomerase trt14
D: Isomerase trt14
E: Isomerase trt14
F: Isomerase trt14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,17719
Polymers109,9416
Non-polymers3,23613
Water12,953719
1
A: Isomerase trt14
D: Isomerase trt14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7527
Polymers36,6472
Non-polymers1,1055
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-19 kcal/mol
Surface area13020 Å2
MethodPISA
2
B: Isomerase trt14
C: Isomerase trt14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7126
Polymers36,6472
Non-polymers1,0654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-12 kcal/mol
Surface area12990 Å2
MethodPISA
3
E: Isomerase trt14
F: Isomerase trt14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7126
Polymers36,6472
Non-polymers1,0654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-18 kcal/mol
Surface area12710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.520, 47.530, 121.210
Angle α, β, γ (deg.)90.00, 108.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Isomerase trt14 / Terretonin synthesis protein 14


Mass: 18323.566 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus terreus NIH 2624 (mold) / Strain: NIH 2624 / Gene: trt14, ATEG_10082 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q0C8A2
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-7X0 / (1R,2S,4aS,4bS,8aS,10S,10aS)-2-[(2S)-3-methoxy-2-methyl-2-oxidanyl-3-oxidanylidene-propanoyl]-2,3,4b,8,8,10a-hexamethyl-10-oxidanyl-7,9-bis(oxidanylidene)-1,4a,5,6,8a,10-hexahydrophenanthrene-1-carboxylic acid


Mass: 492.559 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C26H36O9
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 719 / 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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100mM Imidazole (pH 8.0), 10% PEG 8000, 100mM Ca(OAc)2, 2% 1-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 85146 / % possible obs: 99.1 % / Redundancy: 3.74 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 8.92
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 2.32 / CC1/2: 0.828 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WQF

5wqf


Resolution: 1.899→47.3 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2357 4258 5 %
Rwork0.1983 --
obs0.2002 85141 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.899→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6703 0 217 719 7639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097050
X-RAY DIFFRACTIONf_angle_d1.1919614
X-RAY DIFFRACTIONf_dihedral_angle_d15.7264687
X-RAY DIFFRACTIONf_chiral_restr0.0821103
X-RAY DIFFRACTIONf_plane_restr0.0061222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8987-1.92020.32321200.28222277X-RAY DIFFRACTION86
1.9202-1.94280.28451420.27212702X-RAY DIFFRACTION100
1.9428-1.96650.28721440.24132733X-RAY DIFFRACTION100
1.9665-1.99140.24681400.23472663X-RAY DIFFRACTION99
1.9914-2.01760.33951410.23432670X-RAY DIFFRACTION100
2.0176-2.04530.27321420.23052707X-RAY DIFFRACTION100
2.0453-2.07450.30911430.22672710X-RAY DIFFRACTION100
2.0745-2.10540.24381410.22262676X-RAY DIFFRACTION100
2.1054-2.13830.2321420.21862694X-RAY DIFFRACTION100
2.1383-2.17340.26321440.20752734X-RAY DIFFRACTION100
2.1734-2.21090.25311400.20372670X-RAY DIFFRACTION100
2.2109-2.25110.27131430.20792723X-RAY DIFFRACTION100
2.2511-2.29440.24281420.20792690X-RAY DIFFRACTION100
2.2944-2.34120.2241410.20282682X-RAY DIFFRACTION100
2.3412-2.39210.23551430.20282713X-RAY DIFFRACTION100
2.3921-2.44780.22811420.20322694X-RAY DIFFRACTION100
2.4478-2.5090.24571430.19352729X-RAY DIFFRACTION100
2.509-2.57680.22321420.19982683X-RAY DIFFRACTION100
2.5768-2.65260.27321440.20862741X-RAY DIFFRACTION100
2.6526-2.73820.27941410.2192673X-RAY DIFFRACTION100
2.7382-2.83610.26161440.21262747X-RAY DIFFRACTION100
2.8361-2.94960.24991430.20722723X-RAY DIFFRACTION100
2.9496-3.08380.25631420.21292690X-RAY DIFFRACTION100
3.0838-3.24640.27161440.20942739X-RAY DIFFRACTION100
3.2464-3.44970.22721450.18852746X-RAY DIFFRACTION100
3.4497-3.7160.2151430.1832725X-RAY DIFFRACTION100
3.716-4.08980.21541440.17232740X-RAY DIFFRACTION100
4.0898-4.68110.18381450.15422757X-RAY DIFFRACTION100
4.6811-5.89590.20221460.17982772X-RAY DIFFRACTION100
5.8959-47.3150.18991420.19522680X-RAY DIFFRACTION93

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