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- PDB-7br0: Crystal structure of AclR, a thioredoxin oxidoreductase fold prot... -

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Basic information

Entry
Database: PDB / ID: 7br0
TitleCrystal structure of AclR, a thioredoxin oxidoreductase fold protein carrying the CXXH catalytic motif
ComponentsPyr_redox_2 domain-containing protein
KeywordsOXIDOREDUCTASE / thioredoxin oxidoreductase
Function / homologyFAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily / oxidoreductase activity / FLAVIN-ADENINE DINUCLEOTIDE / Pyr_redox_2 domain-containing protein
Function and homology information
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.003 Å
AuthorsHara, K. / Hashimoto, H. / Maeda, N. / Watanabe, K. / Hertweck, C. / Tsunematsu, Y.
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Specialized Flavoprotein Promotes Sulfur Migration and Spiroaminal Formation in Aspirochlorine Biosynthesis.
Authors: Tsunematsu, Y. / Maeda, N. / Sato, M. / Hara, K. / Hashimoto, H. / Watanabe, K. / Hertweck, C.
History
DepositionMar 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyr_redox_2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8602
Polymers37,0751
Non-polymers7861
Water3,441191
1
A: Pyr_redox_2 domain-containing protein
hetero molecules

A: Pyr_redox_2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7214
Polymers74,1492
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area8190 Å2
ΔGint-50 kcal/mol
Surface area25630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.959, 57.959, 199.865
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-649-

HOH

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Components

#1: Protein Pyr_redox_2 domain-containing protein / AclR


Mass: 37074.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus (strain ATCC 200026 / FGSC A1120 / NRRL 3357 / JCM 12722 / SRRC 167) (mold)
Gene: AFLA_064480 / Production host: Escherichia coli (E. coli) / References: UniProt: B8NI43
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 6000, MES, Lithium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→19.59 Å / Num. obs: 23864 / % possible obs: 99.8 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rrim(I) all: 0.106 / Net I/σ(I): 20.61
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.661 / Num. unique obs: 2298 / CC1/2: 0.936

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NTC

4ntc


Resolution: 2.003→19.586 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.69
RfactorNum. reflection% reflection
Rfree0.2162 1158 4.85 %
Rwork0.1697 --
obs0.1719 23860 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.003→19.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2468 0 53 191 2712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042584
X-RAY DIFFRACTIONf_angle_d0.8053512
X-RAY DIFFRACTIONf_dihedral_angle_d14.951923
X-RAY DIFFRACTIONf_chiral_restr0.032379
X-RAY DIFFRACTIONf_plane_restr0.003453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.003-2.09390.25661350.18532735X-RAY DIFFRACTION99
2.0939-2.20420.23221470.17282770X-RAY DIFFRACTION100
2.2042-2.34210.22071280.17172799X-RAY DIFFRACTION100
2.3421-2.52260.22541350.16722811X-RAY DIFFRACTION100
2.5226-2.77580.24161340.1832829X-RAY DIFFRACTION100
2.7758-3.1760.21891600.18632825X-RAY DIFFRACTION100
3.176-3.99580.22561540.16572869X-RAY DIFFRACTION100
3.9958-19.5860.18461650.15523064X-RAY DIFFRACTION100

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