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- PDB-2gas: Crystal Structure of Isoflavone Reductase -

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Basic information

Entry
Database: PDB / ID: 2gas
TitleCrystal Structure of Isoflavone Reductase
Componentsisoflavone reductase
KeywordsOXIDOREDUCTASE / NADPH-dependent Reductase
Function / homology
Function and homology information


2'-hydroxyisoflavone reductase / 2'-hydroxyisoflavone reductase activity / lignan biosynthetic process / defense response
Similarity search - Function
Phenylcoumaran benzylic ether reductase-like / : / NmrA-like domain / NmrA-like family / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold ...Phenylcoumaran benzylic ether reductase-like / : / NmrA-like domain / NmrA-like family / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Isoflavone reductase
Similarity search - Component
Biological speciesMedicago sativa (alfalfa)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWang, X. / He, X. / Lin, J. / Shao, H. / Chang, Z. / Dixon, R.A.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of Isoflavone Reductase from Alfalfa (Medicago sativa L.)
Authors: Wang, X. / He, X. / Lin, J. / Shao, H. / Chang, Z. / Dixon, R.A.
History
DepositionMar 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: isoflavone reductase
B: isoflavone reductase


Theoretical massNumber of molelcules
Total (without water)68,6022
Polymers68,6022
Non-polymers00
Water16,250902
1
A: isoflavone reductase


Theoretical massNumber of molelcules
Total (without water)34,3011
Polymers34,3011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: isoflavone reductase


Theoretical massNumber of molelcules
Total (without water)34,3011
Polymers34,3011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)176.064, 53.000, 74.397
Angle α, β, γ (deg.)90.00, 112.72, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-445-

HOH

DetailsThe biological assembly is a monomer

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Components

#1: Protein isoflavone reductase


Mass: 34300.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago sativa (alfalfa) / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P52575
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 902 / 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: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4M sodium citrate, 0.1M HEPES, 2% Pluronic F-68, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 1, 2005
RadiationMonochromator: OSMIC CONFOCAL MAX-FLUX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→81 Å / Num. all: 82425 / Num. obs: 82425 / % possible obs: 98.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 24.8
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.9 / Num. unique all: 7849 / % possible all: 94.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QYC

1qyc


Resolution: 1.6→81 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.226 8030 RANDOM
Rwork0.193 --
all0.196 80106 -
obs0.196 80106 -
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.6→81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4840 0 0 902 5742
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection
Rfree0.331 1171
Rwork0.3 -
obs-11109

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