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- PDB-9wtk: Crystal structure of monoalkyl phthalate hydrolase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 9wtk
TitleCrystal structure of monoalkyl phthalate hydrolase in complex with MBP from Rhodococcus sp. EG-5
ComponentsMono-ethylhexylphthalate hydrolase
KeywordsHYDROLASE / Mono-butyl phthalate
Function / homology
Function and homology information


hydrolase activity / membrane
Similarity search - Function
: / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
1-BUTANOL / MALONATE ION / DI(HYDROXYETHYL)ETHER / PHTHALIC ACID / Mono-ethylhexylphthalate hydrolase
Similarity search - Component
Biological speciesRhodococcus sp. EG-5 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsAggarwal, S. / Jangid, K. / Singh, S. / Sharma, A.K. / Kumar, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: To Be Published
Title: Crystal structure of monoalkyl phthalate hydrolase in complex with MBP from Rhodococcus sp. EG-5
Authors: Aggarwal, S. / Jangid, K. / Singh, S. / Sharma, A.K. / Kumar, P.
History
DepositionSep 16, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 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: Mono-ethylhexylphthalate hydrolase
B: Mono-ethylhexylphthalate hydrolase
C: Mono-ethylhexylphthalate hydrolase
D: Mono-ethylhexylphthalate hydrolase
E: Mono-ethylhexylphthalate hydrolase
F: Mono-ethylhexylphthalate hydrolase
G: Mono-ethylhexylphthalate hydrolase
H: Mono-ethylhexylphthalate hydrolase
I: Mono-ethylhexylphthalate hydrolase
J: Mono-ethylhexylphthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)341,208130
Polymers330,66510
Non-polymers10,543120
Water724
1
A: Mono-ethylhexylphthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,19213
Polymers33,0661
Non-polymers1,12512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mono-ethylhexylphthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,32618
Polymers33,0661
Non-polymers1,25917
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mono-ethylhexylphthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,86110
Polymers33,0661
Non-polymers7959
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Mono-ethylhexylphthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,42216
Polymers33,0661
Non-polymers1,35615
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Mono-ethylhexylphthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,22413
Polymers33,0661
Non-polymers1,15712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Mono-ethylhexylphthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,30015
Polymers33,0661
Non-polymers1,23314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Mono-ethylhexylphthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,15414
Polymers33,0661
Non-polymers1,08713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Mono-ethylhexylphthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6498
Polymers33,0661
Non-polymers5837
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Mono-ethylhexylphthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,90510
Polymers33,0661
Non-polymers8399
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Mono-ethylhexylphthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,17613
Polymers33,0661
Non-polymers1,10912
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)176.313, 244.890, 192.097
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-y+1/2,z

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Components

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Protein , 1 types, 10 molecules ABCDEFGHIJ

#1: Protein
Mono-ethylhexylphthalate hydrolase


Mass: 33066.473 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. EG-5 (bacteria) / Gene: mehpH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0U5ADH4

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Non-polymers , 6 types, 124 molecules

#2: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 61 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PHT / PHTHALIC ACID


Mass: 166.131 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C8H6O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-1BO / 1-BUTANOL / BUTAN-1-OL


Mass: 74.122 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.14 Å3/Da / Density % sol: 60.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium sulfate heptahydrate, 20% w/v PEG 3350, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jun 19, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.8→24.74 Å / Num. obs: 101798 / % possible obs: 99.8 % / Redundancy: 9.9 % / Biso Wilson estimate: 22.05 Å2 / CC1/2: 0.972 / Net I/σ(I): 7.8
Reflection shellResolution: 2.8→2.85 Å / Num. unique obs: 4996 / CC1/2: 0.855

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→24.29 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 27.23 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2864 4987 4.9 %
Rwork0.2569 --
obs0.2584 101732 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→24.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22221 0 701 4 22926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223333
X-RAY DIFFRACTIONf_angle_d0.56231407
X-RAY DIFFRACTIONf_dihedral_angle_d14.0178418
X-RAY DIFFRACTIONf_chiral_restr0.0443463
X-RAY DIFFRACTIONf_plane_restr0.0054042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.830.36551710.33157X-RAY DIFFRACTION100
2.83-2.870.39591500.30343240X-RAY DIFFRACTION100
2.87-2.90.35041690.30423176X-RAY DIFFRACTION100
2.9-2.940.2881540.28973207X-RAY DIFFRACTION100
2.94-2.980.30371720.28963194X-RAY DIFFRACTION100
2.98-3.020.33381680.3023219X-RAY DIFFRACTION100
3.02-3.060.41631510.30843207X-RAY DIFFRACTION100
3.06-3.10.34761590.30363188X-RAY DIFFRACTION100
3.1-3.150.34041660.2963223X-RAY DIFFRACTION100
3.15-3.20.33211830.28273205X-RAY DIFFRACTION100
3.2-3.260.2961590.28043198X-RAY DIFFRACTION100
3.26-3.320.33381820.28753178X-RAY DIFFRACTION100
3.32-3.380.31931600.28413213X-RAY DIFFRACTION100
3.38-3.450.33051480.26493221X-RAY DIFFRACTION100
3.45-3.530.31761540.27243227X-RAY DIFFRACTION100
3.53-3.610.2981700.26623203X-RAY DIFFRACTION100
3.61-3.70.29751830.26113226X-RAY DIFFRACTION100
3.7-3.80.27081790.2533184X-RAY DIFFRACTION100
3.8-3.910.27241620.2593208X-RAY DIFFRACTION100
3.91-4.030.26771780.24713215X-RAY DIFFRACTION100
4.03-4.180.25571740.243222X-RAY DIFFRACTION100
4.18-4.340.26131480.23943253X-RAY DIFFRACTION100
4.34-4.540.2471900.23353216X-RAY DIFFRACTION100
4.54-4.780.25491620.2313249X-RAY DIFFRACTION100
4.78-5.070.24351810.22253214X-RAY DIFFRACTION100
5.08-5.460.23651530.2273269X-RAY DIFFRACTION100
5.46-60.28211860.2363249X-RAY DIFFRACTION100
6.01-6.860.23991490.23713311X-RAY DIFFRACTION100
6.86-8.570.21441530.2033314X-RAY DIFFRACTION100
8.58-24.290.17851730.18353359X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -75.8523 Å / Origin y: -34.9219 Å / Origin z: 29.7239 Å
111213212223313233
T0.1428 Å2-0.0021 Å2-0.0298 Å2-0.1322 Å20.0012 Å2--0.1182 Å2
L0.0611 °20.0047 °2-0.0785 °2-0.0224 °20.0042 °2--0.0553 °2
S0.0036 Å °-0.0175 Å °-0.0095 Å °-0.0119 Å °-0.0129 Å °-0.0024 Å °-0.0789 Å °-0.0129 Å °0.0032 Å °
Refinement TLS groupSelection details: all

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