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- PDB-8ea1: Structure of kudzu 2-hydroxyisoflavanone dehydratase in complex w... -

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Basic information

Entry
Database: PDB / ID: 8ea1
TitleStructure of kudzu 2-hydroxyisoflavanone dehydratase in complex with P-NITROPHENOL
Components2-hydroxyisoflavanone dehydratase
KeywordsPLANT PROTEIN / dehydratase / dehydration / carboxylesterase / Pueraria lobata
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 / P-NITROPHENOL / 2-hydroxyisoflavanone dehydratase
Function and homology information
Biological speciesPueraria montana var. lobata (kudzu vine)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.29 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0592
Polymers38,9201
Non-polymers1391
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.844, 102.844, 70.280
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: Chemical ChemComp-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.01 Å3/Da / Density % sol: 59.12 %
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: Mar 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 19522 / % possible obs: 99.8 % / Redundancy: 10.9 % / Biso Wilson estimate: 51.67 Å2 / CC1/2: 0.86 / Rmerge(I) obs: 0.054 / Net I/σ(I): 42.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 5 / Num. unique obs: 1912 / CC1/2: 0.78 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O7R

2o7r


Resolution: 2.29→30.36 Å / SU ML: 0.2849 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.719
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.201 996 5.12 %
Rwork0.1806 18471 -
obs0.1816 19467 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.36 Å2
Refinement stepCycle: LAST / Resolution: 2.29→30.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2442 0 10 83 2535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782522
X-RAY DIFFRACTIONf_angle_d1.12733441
X-RAY DIFFRACTIONf_chiral_restr0.077377
X-RAY DIFFRACTIONf_plane_restr0.0046450
X-RAY DIFFRACTIONf_dihedral_angle_d12.7366891
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.420.31631420.23432600X-RAY DIFFRACTION99.53
2.42-2.570.2631480.21792588X-RAY DIFFRACTION99.64
2.57-2.760.24521480.21432606X-RAY DIFFRACTION99.82
2.76-3.040.27241320.22282639X-RAY DIFFRACTION99.89
3.04-3.480.21381410.20762635X-RAY DIFFRACTION99.93
3.48-4.380.17441550.16552652X-RAY DIFFRACTION100
4.39-30.360.1691300.15252751X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 34.4561170985 Å / Origin y: 14.8050858067 Å / Origin z: -0.543461019972 Å
111213212223313233
T0.460447951088 Å20.0191170025425 Å20.101885832736 Å2-0.416449895998 Å20.0268645761977 Å2--0.395231597061 Å2
L1.2982571632 °2-0.189594364614 °20.0533687960472 °2-2.81790449696 °2-0.166227562818 °2--1.73148909426 °2
S0.092220376744 Å °-0.0954606533257 Å °-0.0396851855379 Å °0.668837990138 Å °-0.0337740446324 Å °0.323270395683 Å °-0.174693690366 Å °-0.372900510501 Å °-0.0539854713795 Å °
Refinement TLS groupSelection details: all

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