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- PDB-6jxn: Crystal Structure of Indigo reductase from Bacillus smithii type ... -

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Basic information

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


Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor / FMN-dependent NADH-azoreductase / 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: 1.97 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)105,47213
Polymers102,2844
Non-polymers3,1889
Water8,395466
1
A: FMN-dependent NADH-azoreductase
D: FMN-dependent NADH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6326
Polymers51,1422
Non-polymers1,4904
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-35 kcal/mol
Surface area18700 Å2
MethodPISA
2
B: FMN-dependent NADH-azoreductase
C: FMN-dependent NADH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8407
Polymers51,1422
Non-polymers1,6985
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-25 kcal/mol
Surface area18390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.480, 105.140, 87.780
Angle α, β, γ (deg.)90.00, 92.49, 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: 25570.969 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: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H17NO3S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 2.39 Å3/Da / Density % sol: 43.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 40% PEG 600, 0.1 M CHES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→35.62 Å / Num. obs: 62256 / % possible obs: 99.9 % / Redundancy: 5 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.159 / Net I/σ(I): 9.8
Reflection shellResolution: 1.97→2 Å / Redundancy: 4 % / Rmerge(I) obs: 0.061 / Num. unique obs: 9820 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
CNS1.3refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W78

3w78


Resolution: 1.97→35.62 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.1858 3132 5 %Random selection
Rwork0.1779 ---
obs-62041 99.9 %-
Displacement parametersBiso mean: 22 Å2
Refinement stepCycle: LAST / Resolution: 1.97→35.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6594 0 213 466 7273
LS refinement shellResolution: 1.97→2 Å /
Rfactor% reflection
Rfree0.186 -
Rwork0.178 -
obs-99.9 %

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