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- PDB-9vmw: The crystal structure of the Phthalate Hydrolase EstJ6 in complex... -

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Basic information

Entry
Database: PDB / ID: 9vmw
TitleThe crystal structure of the Phthalate Hydrolase EstJ6 in complex with phthalic acid
ComponentsEsterase
KeywordsHYDROLASE / Phthalic acid esters / Phthalate Hydrolase / phthalic acid
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
PHTHALIC ACID / Esterase
Similarity search - Component
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWang, Y.H. / Chen, Y.B. / Hu, R.K.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930084 China
National Natural Science Foundation of China (NSFC)31972014 China
CitationJournal: To Be Published
Title: Crystal structure of the Phthalate Hydrolase EstJ6 in complex with phthalic acid at 1.9 Angstroms resolution
Authors: Chen, Y.B. / Wang, Y.H. / 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

Downloads & links

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Assembly

Deposited unit
A: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3412
Polymers32,1751
Non-polymers1661
Water4,432246
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)64.417, 120.758, 96.508
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-554-

HOH

21A-721-

HOH

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Components

#1: Protein Esterase


Mass: 32175.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P8L7K3, carboxylesterase
#2: Chemical ChemComp-PHT / PHTHALIC ACID


Mass: 166.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.92 Å3/Da / Density % sol: 57.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 2.4 mol/L CH2(CO2Na)2

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Data collection

DiffractionMean temperature: 289 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 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: 1.8→56.84 Å / Num. obs: 35417 / % possible obs: 100 % / Redundancy: 12.4 % / CC1/2: 0.997 / Net I/σ(I): 11.7
Reflection shellResolution: 1.8→1.89 Å / Num. unique obs: 5114 / CC1/2: 0.863

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→37.695 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1843 1013 3.38 %
Rwork0.1484 --
obs0.1495 30005 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→37.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2174 0 12 246 2432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072235
X-RAY DIFFRACTIONf_angle_d1.0043039
X-RAY DIFFRACTIONf_dihedral_angle_d14.409823
X-RAY DIFFRACTIONf_chiral_restr0.044341
X-RAY DIFFRACTIONf_plane_restr0.006397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.00020.20861460.17864049X-RAY DIFFRACTION100
2.0002-2.12550.19931340.16194089X-RAY DIFFRACTION100
2.1255-2.28960.19311470.14974127X-RAY DIFFRACTION100
2.2896-2.51990.1881470.15574106X-RAY DIFFRACTION100
2.5199-2.88450.21261410.15814131X-RAY DIFFRACTION100
2.8845-3.63370.16561470.15094168X-RAY DIFFRACTION100
3.6337-37.6950.17711510.13364322X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.09412.1081-1.0899.8297-3.48733.54040.37130.44070.6760.35730.14080.7503-0.4712-0.5-0.51450.33680.08610.09080.5107-0.03570.4702-33.0091-11.689114.6145
21.2506-1.46291.49588.0113-7.12646.3893-0.0072-0.31090.04610.80330.27050.5189-0.5332-0.5346-0.27570.4356-0.02090.06540.3987-0.04670.295-19.6565-9.563618.3685
32.15670.57570.01511.4735-0.39521.76530.0767-0.3595-0.04310.2552-0.1275-0.1012-0.04120.02540.06140.2127-0.0178-0.02990.241-0.00070.2142-9.5931-18.650315.0681
41.57280.2071-0.07771.84330.27720.87570.0219-0.0728-0.1102-0.00870.0044-0.13310.06750.0928-0.03510.1860.0081-0.02660.19430.00120.2216-7.1497-22.46923.7149
51.20930.21920.38411.8840.15431.5542-0.00190.18330.0081-0.2068-0.0510.2116-0.1194-0.16840.05060.19380.0256-0.02540.1909-0.01060.2224-20.4161-13.9442-3.4999
63.3329-1.9011-1.05451.95-0.06841.65480.10390.3083-0.3903-0.1368-0.14460.28560.056-0.22580.09550.1903-0.0175-0.04880.2543-0.07490.2961-22.3547-25.8567-2.0834
71.42010.4526-0.22730.625-0.18621.8460.0646-0.1149-0.23490.186-0.13220.11240.2163-0.16690.0660.2386-0.0575-0.01340.24-0.01160.311-22.8446-29.12911.0119
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 46 )
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 117 )
4X-RAY DIFFRACTION4chain 'A' and (resid 118 through 183 )
5X-RAY DIFFRACTION5chain 'A' and (resid 184 through 230 )
6X-RAY DIFFRACTION6chain 'A' and (resid 231 through 256 )
7X-RAY DIFFRACTION7chain 'A' and (resid 257 through 297 )

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