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

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Basic information

Entry
Database: PDB / ID: 9vmu
TitleThe crystal structure of the Phthalate Hydrolase EstJ6 in complex with monobutyl phthalate
ComponentsEsterase
KeywordsHYDROLASE / Phthalic acid esters / Phthalate Hydrolase / monobutyl phthalate
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: 2.3 Å
AuthorsWang, Y.H. / Chen, Y.B. / Hu, R.H.
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 monobutyl phthalate at 2.3 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

Downloads & links

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Assembly

Deposited unit
A: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3972
Polymers32,1751
Non-polymers2221
Water90150
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)64.263, 64.263, 206.159
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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-A1ESU / 2-butoxycarbonylbenzoic acid


Mass: 222.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 3.31 Å3/Da / Density % sol: 62.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 50% (v/v) TacsimateTM (pH 7.0)

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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 31, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.1→61.35 Å / Num. obs: 25495 / % possible obs: 96.4 % / Redundancy: 24.2 % / CC1/2: 0.999 / Net I/σ(I): 20.8
Reflection shellResolution: 2.1→2.21 Å / Num. unique obs: 3780 / CC1/2: 0.86

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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: 2.3→34.703 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1999 1366 6.92 %
Rwork0.1633 --
obs0.1658 19754 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→34.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 0 16 50 2258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082258
X-RAY DIFFRACTIONf_angle_d1.0993072
X-RAY DIFFRACTIONf_dihedral_angle_d15.255828
X-RAY DIFFRACTIONf_chiral_restr0.04345
X-RAY DIFFRACTIONf_plane_restr0.006402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.38220.22561340.18961809X-RAY DIFFRACTION100
2.3822-2.47750.22321360.20191838X-RAY DIFFRACTION100
2.4775-2.59030.26511350.19881815X-RAY DIFFRACTION100
2.5903-2.72680.24631130.21031516X-RAY DIFFRACTION83
2.7268-2.89750.25151370.20151844X-RAY DIFFRACTION100
2.8975-3.12110.28361380.2051854X-RAY DIFFRACTION100
3.1211-3.4350.22781370.21081853X-RAY DIFFRACTION100
3.435-3.93140.22771410.16341892X-RAY DIFFRACTION100
3.9314-4.95090.17211420.12911920X-RAY DIFFRACTION100
4.9509-34.7030.14141530.13192047X-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)
13.0707-0.7724-1.51943.3791.14413.27820.3025-0.4974-1.03610.4006-0.10680.82310.3614-0.5043-0.22370.7177-0.079-0.07040.50880.14020.67759.5157-46.4773-3.3023
25.3876-0.29890.0572.515-0.42381.9865-0.397-0.1865-0.75560.51780.37460.15670.0542-0.5314-0.0330.72160.060.05760.66160.06780.46119.612-33.12111.1581
32.0292-0.07710.58572.6402-0.81841.8516-0.1602-0.29530.17270.560.08670.115-0.4556-0.11530.06210.62720.0894-0.09080.335-0.02860.397314.1819-21.0102-10.6048
41.5859-0.06960.47341.3283-0.35742.20370.0614-0.2476-0.2606-0.160.09420.54450.2764-0.6427-0.1790.504-0.0639-0.12410.51370.07620.6282.5612-33.247-18.6111
51.38440.508-0.20941.7529-0.22251.5105-0.21370.2088-0.2663-0.58810.21460.28690.2594-0.23880.06340.5857-0.0453-0.11340.32680.01520.438310.465-33.255-25.8966
61.2078-0.70991.0412.1257-0.59681.3047-0.028-0.0589-0.1953-0.22870.1368-0.01940.40450.1112-0.04320.51840.0169-0.05570.3339-0.0040.352221.5683-36.3062-15.8907
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 161 )
4X-RAY DIFFRACTION4chain 'A' and (resid 162 through 220 )
5X-RAY DIFFRACTION5chain 'A' and (resid 221 through 256 )
6X-RAY DIFFRACTION6chain 'A' and (resid 257 through 297 )

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