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- PDB-8ea2: Structure of 2-hydroxyisoflavanone dehydratase from Pueraria lobate -

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Basic information

Entry
Database: PDB / ID: 8ea2
TitleStructure of 2-hydroxyisoflavanone dehydratase from Pueraria lobate
Components2-hydroxyisoflavanone dehydratase
KeywordsPLANT PROTEIN / dehydratase / dehydration / carboxylesterase
Function / homologyLipase, GDXG, putative histidine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold / hydrolase activity / 2-hydroxyisoflavanone dehydratase
Function and homology information
Biological speciesPueraria montana var. lobata (kudzu vine)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.394 Å
AuthorsPan, H. / Wang, X.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Commun Biol / Year: 2022
Title: The protein conformational basis of isoflavone biosynthesis.
Authors: Wang, X. / Pan, H. / Sagurthi, S. / Paris, V. / Zhuo, C. / Dixon, R.A.
History
DepositionAug 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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: 2-hydroxyisoflavanone dehydratase


Theoretical massNumber of molelcules
Total (without water)38,9201
Polymers38,9201
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.309, 102.309, 70.239
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein 2-hydroxyisoflavanone dehydratase /


Mass: 38919.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pueraria montana var. lobata (kudzu vine)
Plasmid: pDEST17 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E9M5G1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.73 Å3/Da / Density % sol: 59.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 18% PEG3350, 0.1 M HEPES pH7.5

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.394→50 Å / Num. obs: 16673 / % possible obs: 98 % / Redundancy: 6 % / Biso Wilson estimate: 55.7903308066 Å2 / CC1/2: 0.83 / Rmerge(I) obs: 0.083 / Net I/σ(I): 14.8
Reflection shellResolution: 2.394→2.49 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1693 / CC1/2: 0.78 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O7R

2o7r


Resolution: 2.394→24.24 Å / SU ML: 0.301290171736 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.7781019266
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2433 840 5.05841262194 %
Rwork0.1864 15766 -
obs0.189 16606 97.4931016263 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.75864869 Å2
Refinement stepCycle: LAST / Resolution: 2.394→24.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2455 0 0 78 2533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008630579482442525
X-RAY DIFFRACTIONf_angle_d1.274213111493446
X-RAY DIFFRACTIONf_chiral_restr0.077562942312380
X-RAY DIFFRACTIONf_plane_restr0.00464356693409450
X-RAY DIFFRACTIONf_dihedral_angle_d16.6082411159899
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.394-2.54430.3248210244671390.2470439053792609X-RAY DIFFRACTION98.002853067
2.5443-2.74050.3302948597751440.2282491289542642X-RAY DIFFRACTION99.820852741
2.7405-3.01590.289153800031670.2288759130052640X-RAY DIFFRACTION99.7158081705
3.0159-3.45120.2623711190131450.2138265764092647X-RAY DIFFRACTION99.1125310614
3.4512-4.3440.2613490465621200.1726925768962569X-RAY DIFFRACTION94.317783234
4.344-24.2360.1799252799731250.1605971032132659X-RAY DIFFRACTION94.3089430894
Refinement TLS params.Method: refined / Origin x: -33.9760377247 Å / Origin y: -14.711700184 Å / Origin z: -0.421264521459 Å
111213212223313233
T0.43989794527 Å20.0236749237967 Å2-0.0592254002641 Å2-0.389331399588 Å2-0.00858809528218 Å2--0.392613020996 Å2
L1.38139731895 °20.106010772414 °20.0524302778501 °2-2.50577539872 °20.205855344706 °2--1.52989899234 °2
S0.0631096583749 Å °-0.0777100326735 Å °0.0614794476141 Å °0.486947176773 Å °-0.030664937724 Å °-0.242922987081 Å °0.0489881630524 Å °0.246014394201 Å °-0.0406279437315 Å °
Refinement TLS groupSelection details: all

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