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- PDB-9vmr: Crystal structure of Phthalate Hydrolase EstJ6 -

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Basic information

Entry
Database: PDB / ID: 9vmr
TitleCrystal structure of Phthalate Hydrolase EstJ6
ComponentsEsterase
KeywordsHYDROLASE / Phthalic acid esters / Bioremediation / bifunctional hydrolase / Plasticizer
Function / homology
Function and homology information


carboxylesterase / carboxylesterase activity / triacylglycerol lipase activity
Similarity search - Function
Lipase, GDXG, putative histidine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. / Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative serine active site. / : / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsWang, Y.H. / Chen, Y.B. / Hu, R.K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930084 China
CitationJournal: To Be Published
Title: Structural of bifunctional Phthalate Hydrolase EstJ6 at 1.8 Angstroms resolution.
Authors: Wang, Y.H. / Chen, Y.B. / Hu, R.K.
History
DepositionJun 29, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Esterase


Theoretical massNumber of molelcules
Total (without water)32,1761
Polymers32,1761
Non-polymers00
Water5,999333
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.297, 120.861, 97.969
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-690-

HOH

21A-694-

HOH

31A-722-

HOH

41A-726-

HOH

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Components

#1: Protein Esterase


Mass: 32176.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A4P8L7K3, carboxylesterase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.96 Å3/Da / Density % sol: 58.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 1.6 mol/L (NH4)2SO4, 0.1 mol/L HEPES (pH 6.6), and 0.5% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Aug 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 37718 / % possible obs: 99.5 % / Redundancy: 13.2 % / CC1/2: 0.991 / Net I/σ(I): 28.45
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 11.8 % / Num. unique obs: 1878 / CC1/2: 0.973 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→34.16 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.9 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17775 1876 5 %RANDOM
Rwork0.14999 ---
obs0.15136 35923 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.112 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20 Å2-0 Å2
2---0.44 Å2-0 Å2
3----0.82 Å2
Refinement stepCycle: 1 / Resolution: 1.76→34.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2174 0 0 333 2507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122223
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162165
X-RAY DIFFRACTIONr_angle_refined_deg1.8281.8073023
X-RAY DIFFRACTIONr_angle_other_deg0.6461.7445003
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7455293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.015511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30910359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1060.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022612
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02450
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1492.2631175
X-RAY DIFFRACTIONr_mcbond_other2.1492.2621175
X-RAY DIFFRACTIONr_mcangle_it2.7024.0581467
X-RAY DIFFRACTIONr_mcangle_other2.7084.061468
X-RAY DIFFRACTIONr_scbond_it4.0112.6771048
X-RAY DIFFRACTIONr_scbond_other4.0092.6771049
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8974.6781557
X-RAY DIFFRACTIONr_long_range_B_refined7.19823.872649
X-RAY DIFFRACTIONr_long_range_B_other6.79621.922521
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.761→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 143 -
Rwork0.211 2581 -
obs--97.53 %

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