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- PDB-1z48: Crystal structure of reduced YqjM from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 1z48
TitleCrystal structure of reduced YqjM from Bacillus subtilis
ComponentsProbable NADH-dependent flavin oxidoreductase yqjM
KeywordsOXIDOREDUCTASE / flavin / FMN / beta-alpha-barrel
Function / homology
Function and homology information


NADPH dehydrogenase / pentaerythritol trinitrate reductase activity / NADPH dehydrogenase activity / response to toxic substance / FMN binding / NADP binding
Similarity search - Function
NADPH dehydrogenase, bacteria / NADPH dehydrogenase YqjM-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / NADPH dehydrogenase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKitzing, K. / Fitzpatrick, T.B. / Wilken, C. / Sawa, J. / Bourenkov, G.P. / Macheroux, P. / Clausen, T.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: The 1.3 A Crystal Structure of the Flavoprotein YqjM Reveals a Novel Class of Old Yellow Enzymes
Authors: Kitzing, K. / Fitzpatrick, T.B. / Wilken, C. / Sawa, J. / Bourenkov, G.P. / Macheroux, P. / Clausen, T.
History
DepositionMar 15, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable NADH-dependent flavin oxidoreductase yqjM
B: Probable NADH-dependent flavin oxidoreductase yqjM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2064
Polymers76,2932
Non-polymers9132
Water12,052669
1
A: Probable NADH-dependent flavin oxidoreductase yqjM
B: Probable NADH-dependent flavin oxidoreductase yqjM
hetero molecules

A: Probable NADH-dependent flavin oxidoreductase yqjM
B: Probable NADH-dependent flavin oxidoreductase yqjM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,4118
Polymers152,5864
Non-polymers1,8254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)51.210, 184.573, 168.893
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1825-

HOH

DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operations: -x, y, -z+0.5

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Components

#1: Protein Probable NADH-dependent flavin oxidoreductase yqjM / YqjM


Mass: 38146.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codon-Plus(DE3)-RIL / References: UniProt: P54550, Oxidoreductases
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 669 / 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: 2.66 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Tris/HCl, PEG 3500, lithium sulfate, strontium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 11, 2004
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→10 Å / Num. all: 86971 / Num. obs: 73765 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.96 % / Rsym value: 0.033 / Net I/σ(I): 26.5
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.93 % / Mean I/σ(I) obs: 7 / Num. unique all: 4275 / Rsym value: 0.146 / % possible all: 98.7

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Processing

Software
NameClassification
MOSFLMdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z41

1z41


Resolution: 1.8→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.199 4349 Random
Rwork0.179 --
all0.18 86971 -
obs0.18 73765 -
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5274 0 62 669 6005
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.28
X-RAY DIFFRACTIONc_bond_d0.006

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