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- PDB-6jxs: Crystal Structure of Indigo reductase (Y151F) from Bacillus smith... -

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Basic information

Entry
Database: PDB / ID: 6jxs
TitleCrystal Structure of Indigo reductase (Y151F) from Bacillus smithii type strain DSM 4216
ComponentsFMN-dependent NADH-azoreductase
KeywordsOXIDOREDUCTASE / Indigo reductase / Y151F / Bacillus smithii
Function / homology
Function and homology information


FMN-dependent NADH-azoreductase / Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor / oxidoreductase activity, acting on NAD(P)H as acceptor / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / FMN binding / electron transfer activity
Similarity search - Function
NADH:quinone oxidoreductase, FMN-dependent / : / Flavodoxin-like fold / Flavodoxin-like fold / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / FMN dependent NADH:quinone oxidoreductase
Similarity search - Component
Biological speciesBacillus smithii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsYoneda, K. / Sakuraba, H. / Ohshima, T.
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Structural and biochemical characterization of an extremely thermostable FMN-dependent NADH-indigo reductase from Bacillus smithii.
Authors: Yoneda, K. / Yoshioka, M. / Sakuraba, H. / Araki, T. / Ohshima, T.
History
DepositionApr 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 25, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: FMN-dependent NADH-azoreductase
B: FMN-dependent NADH-azoreductase
C: FMN-dependent NADH-azoreductase
D: FMN-dependent NADH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,78610
Polymers102,2204
Non-polymers2,5666
Water6,792377
1
A: FMN-dependent NADH-azoreductase
C: FMN-dependent NADH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3935
Polymers51,1102
Non-polymers1,2833
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-42 kcal/mol
Surface area18500 Å2
MethodPISA
2
B: FMN-dependent NADH-azoreductase
D: FMN-dependent NADH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3935
Polymers51,1102
Non-polymers1,2833
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-38 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.274, 104.214, 87.724
Angle α, β, γ (deg.)90.00, 92.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
FMN-dependent NADH-azoreductase / Azo-dye reductase / FMN-dependent NADH-azo compound oxidoreductase


Mass: 25554.969 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus smithii (bacteria) / Strain: DSM 4216 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIPL
References: UniProt: G9QLG5, Oxidoreductases; Acting on other nitrogenous compounds as donors
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O9
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.36 Å3/Da / Density % sol: 42.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 36 % PEG600 0.1 M Phosphate-citrate buffer (pH 4.2)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 63458 / % possible obs: 98.9 % / Redundancy: 5 % / Biso Wilson estimate: 10.8 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 20.8
Reflection shellResolution: 1.95→1.97 Å / Rmerge(I) obs: 0.251 / Num. unique obs: 62747

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Processing

Software
NameVersionClassification
HKL-2000data scaling
MOLREPphasing
REFMAC5.8.0158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JXN

6jxn


Resolution: 1.95→33.14 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2066 3148 5 %
Rwork0.1966 --
obs-62459 98.9 %
Displacement parametersBiso mean: 20 Å2
Refinement stepCycle: LAST / Resolution: 1.95→33.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6553 0 174 377 7104
LS refinement shellResolution: 1.95→2.07 Å
RfactorNum. reflection% reflection
Rfree0.202 --
Rwork0.175 --
obs-9944 99.5 %

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