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- PDB-5wqf: Structure of fungal meroterpenoid isomerase Trt14 -

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Basic information

Entry
Database: PDB / ID: 5wqf
TitleStructure of fungal meroterpenoid isomerase Trt14
ComponentsIsomerase trt14
KeywordsISOMERASE / meroterpenoid / terretonin
Function / homology: / Isomerases / terpenoid biosynthetic process / isomerase activity / N-PROPANOL / Isomerase trt14
Function and homology information
Biological speciesAspergillus terreus NIH 2624 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsMori, T. / Iwabuchi, 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 26, 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 1.2Sep 16, 2020Group: Derived calculations / Structure summary / Category: pdbx_struct_conn_angle / struct / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._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_auth_seq_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.title / _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
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)110,48218
Polymers109,9416
Non-polymers54112
Water5,513306
1
A: Isomerase trt14
C: Isomerase trt14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9288
Polymers36,6472
Non-polymers2816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-18 kcal/mol
Surface area13000 Å2
MethodPISA
2
B: Isomerase trt14
D: Isomerase trt14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8276
Polymers36,6472
Non-polymers1804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-15 kcal/mol
Surface area13540 Å2
MethodPISA
3
E: Isomerase trt14
F: Isomerase trt14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7274
Polymers36,6472
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-30 kcal/mol
Surface area13460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.610, 47.660, 121.440
Angle α, β, γ (deg.)90.00, 108.07, 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, Isomerases
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.52 Å3/Da / Density % sol: 51.15 %
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: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 73543 / % possible obs: 98.4 % / Redundancy: 3.42 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 14.2
Reflection shellResolution: 2→2.12 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.57 / CC1/2: 0.92 / % possible all: 97.9

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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: Selenomethionine labeled Trt14

Resolution: 2.001→47.824 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2466 3674 5 %
Rwork0.2138 --
obs0.2155 73499 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.001→47.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6645 0 21 306 6972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076775
X-RAY DIFFRACTIONf_angle_d0.7879151
X-RAY DIFFRACTIONf_dihedral_angle_d16.5212488
X-RAY DIFFRACTIONf_chiral_restr0.0551041
X-RAY DIFFRACTIONf_plane_restr0.0051175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0008-2.02710.33351350.28232572X-RAY DIFFRACTION96
2.0271-2.05490.34041430.28682702X-RAY DIFFRACTION99
2.0549-2.08420.32291390.28112647X-RAY DIFFRACTION99
2.0842-2.11540.36021390.28222623X-RAY DIFFRACTION98
2.1154-2.14840.36481380.28112663X-RAY DIFFRACTION98
2.1484-2.18360.34031390.27142637X-RAY DIFFRACTION97
2.1836-2.22130.31151400.26112657X-RAY DIFFRACTION100
2.2213-2.26170.3141440.25812739X-RAY DIFFRACTION100
2.2617-2.30520.30421400.25722658X-RAY DIFFRACTION99
2.3052-2.35220.3061420.25552692X-RAY DIFFRACTION99
2.3522-2.40340.32681430.25532718X-RAY DIFFRACTION100
2.4034-2.45930.29871410.25352684X-RAY DIFFRACTION99
2.4593-2.52080.27011430.24282714X-RAY DIFFRACTION99
2.5208-2.58890.29011400.22962674X-RAY DIFFRACTION99
2.5889-2.66510.26541420.22632689X-RAY DIFFRACTION98
2.6651-2.75110.27741390.24632644X-RAY DIFFRACTION98
2.7511-2.84940.25051390.23952646X-RAY DIFFRACTION97
2.8494-2.96350.28961460.23262755X-RAY DIFFRACTION100
2.9635-3.09840.28321400.24432684X-RAY DIFFRACTION100
3.0984-3.26170.27211430.23212711X-RAY DIFFRACTION99
3.2617-3.4660.24381430.20872724X-RAY DIFFRACTION99
3.466-3.73350.23091410.19922685X-RAY DIFFRACTION98
3.7335-4.1090.21941390.18572641X-RAY DIFFRACTION96
4.109-4.70310.1661440.16172734X-RAY DIFFRACTION99
4.7031-5.92370.21321450.18032756X-RAY DIFFRACTION99
5.9237-47.83750.18911470.18152776X-RAY DIFFRACTION96

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