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- PDB-1bwk: OLD YELLOW ENZYME (OYE1) MUTANT H191N -

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Basic information

Entry
Database: PDB / ID: 1bwk
TitleOLD YELLOW ENZYME (OYE1) MUTANT H191N
ComponentsPROTEIN (NADPH DEHYDROGENASE 1)
KeywordsOXIDOREDUCTASE / FLAVOENZYME / NADPH OXIDOREDUCTASE / TIM BARREL
Function / homology
Function and homology information


NADPH dehydrogenase / NADPH dehydrogenase activity / FMN binding
Similarity search - Function
Oxidoreductase Oye-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 1
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.3 Å
AuthorsBrown, B.J. / Deng, Z. / Karplus, P.A. / Massey, V.
CitationJournal: J.Biol.Chem. / Year: 1998
Title: On the active site of Old Yellow Enzyme. Role of histidine 191 and asparagine 194.
Authors: Brown, B.J. / Deng, Z. / Karplus, P.A. / Massey, V.
History
DepositionSep 24, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 30, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 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: PROTEIN (NADPH DEHYDROGENASE 1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3312
Polymers44,8741
Non-polymers4561
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.300, 143.300, 43.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PROTEIN (NADPH DEHYDROGENASE 1) / E.C.1.6.99.1 OXIDOREDUCTASE / OLD YELLOW ENZYME 1 / OYE1


Mass: 44874.297 Da / Num. of mol.: 1 / Mutation: H191N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: OYE1 / Plasmid: PET3B / Gene (production host): OYE1-H191N / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE / References: UniProt: Q02899, NADPH dehydrogenase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.46 Å3/Da / Density % sol: 49.97 %
Crystal growpH: 8.3 / Details: pH 8.3
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop / Details: Fox, K.M., (1993) J. Mol. Biol., 234, 502.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mg/mlprotein1drop
210 mMTris-HCl1drop
310 mM1dropNaCl
40.01 Mphrnylmethylsulfonyl fluoride1drop
50.1 MHEPES1reservoir
630 %(v/v)PEG4001reservoir
70.2 M1reservoirMgCl2

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 20012 / % possible obs: 97.1 % / Redundancy: 3.8 % / Rsym value: 0.084 / Net I/σ(I): 12.3
Reflection shellResolution: 2.3→2.4 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.383 / % possible all: 96.1
Reflection
*PLUS
Num. measured all: 76546 / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
% possible obs: 96.1 % / Rmerge(I) obs: 0.383

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 1OYA

1oya


Resolution: 2.3→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.0001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1477 8 %RANDOM
Rwork0.18 ---
obs0.18 17205 75.2 %-
Displacement parametersBiso mean: 21.5 Å2
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3173 0 31 127 3331
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.29
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.367 59 -
Rwork0.265 994 -
obs--43.3 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOL
X-RAY DIFFRACTION3PARAFMN.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 8 % / Rfactor obs: 0.18 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.29
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / Rfactor Rfree: 0.367 / Rfactor Rwork: 0.265

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