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- PDB-8hgv: Crystal structure of monoalkyl phthalate hydrolase MehpH -

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Basic information

Entry
Database: PDB / ID: 8hgv
TitleCrystal structure of monoalkyl phthalate hydrolase MehpH
ComponentsMonoethylhexylphthalate hydrolase
KeywordsHYDROLASE
Function / homology: / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / membrane / Monoethylhexylphthalate hydrolase
Function and homology information
Biological speciesGordonia sp. P8219 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.30006253403 Å
AuthorsZhang, Z.M. / Wang, Y.J. / Chen, Y.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Chem / Year: 2023
Title: Molecular insights into the catalytic mechanism of plasticizer degradation by a monoalkyl phthalate hydrolase.
Authors: Chen, Y. / Wang, Y. / Xu, Y. / Sun, J. / Yang, L. / Feng, C. / Wang, J. / Zhou, Y. / Zhang, Z.M. / Wang, Y.
History
DepositionNov 15, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Monoethylhexylphthalate hydrolase
B: Monoethylhexylphthalate hydrolase


Theoretical massNumber of molelcules
Total (without water)62,7362
Polymers62,7362
Non-polymers00
Water1,31573
1
A: Monoethylhexylphthalate hydrolase

B: Monoethylhexylphthalate hydrolase


Theoretical massNumber of molelcules
Total (without water)62,7362
Polymers62,7362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area1850 Å2
ΔGint-8 kcal/mol
Surface area22320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.69, 128.12, 54.46
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Monoethylhexylphthalate hydrolase


Mass: 31368.205 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gordonia sp. P8219 (bacteria) / Gene: mehpH / Production host: Escherichia coli (E. coli) / References: UniProt: Q2MHH5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.15 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris-HCl pH 7.2, 17% (w/v) PEG 3350 and 200 mM Calcium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2→106.69 Å / Num. obs: 74613 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 21.2 Å2 / CC1/2: 0.977 / Net I/σ(I): 12.6
Reflection shellResolution: 2→2.04 Å / Num. unique obs: 71121 / CC1/2: 0.941

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.30006253403→20.7461692413 Å / SU ML: 0.283873914551 / Cross valid method: FREE R-VALUE / σ(F): 1.34355668287 / Phase error: 24.1517237536
RfactorNum. reflection% reflection
Rfree0.236753120746 1214 4.89338546495 %
Rwork0.196497266182 23595 -
obs0.198440728959 24809 99.8912868417 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.087419704 Å2
Refinement stepCycle: LAST / Resolution: 2.30006253403→20.7461692413 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4268 0 0 73 4341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003093432675424371
X-RAY DIFFRACTIONf_angle_d0.7082009095115957
X-RAY DIFFRACTIONf_chiral_restr0.0255172312517669
X-RAY DIFFRACTIONf_plane_restr0.0032860599542774
X-RAY DIFFRACTIONf_dihedral_angle_d14.07111628031506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.3920.3561083604441370.2896323239592567X-RAY DIFFRACTION100
2.392-2.50070.3140368519921370.2715586382162593X-RAY DIFFRACTION100
2.5007-2.63230.2964189101881290.2655717880762585X-RAY DIFFRACTION100
2.6323-2.79690.2948292702051390.2521905636182584X-RAY DIFFRACTION100
2.7969-3.01220.3010771898141360.2481630291912602X-RAY DIFFRACTION100
3.0122-3.31430.2369878269051290.2224648627992607X-RAY DIFFRACTION100
3.3143-3.79130.2479632708271290.1902873255362638X-RAY DIFFRACTION100
3.7913-4.76710.2206971616411430.1506410088952653X-RAY DIFFRACTION100
4.7671-100.1772162524171350.1705534731352766X-RAY DIFFRACTION99.0778688525
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)
11.84938270650.7844102811230.5529653458093.963769597950.3012033547683.7363013105-0.01319956844980.03193284298050.09726669245270.06944475803570.01866024100330.0324056449469-0.2232562629820.064699241230.009870898001590.2945372731930.02553423276950.009891751780290.3318052458540.02352202379950.34274986005420.693332511456.208710748759.4368513306
23.74350074237-0.578066358191-1.048007231184.39770471122-0.7551968239976.10704103587-0.04593720579070.3534696468210.114544379995-0.43643673518-0.01960761549730.05233041800040.5033841720710.2769220287430.07738800840560.4417990596180.0468647877590.07248471549220.4199642020950.06669771429530.3794979930325.431509303742.941720410857.1073407184
32.66703770937-3.384052672742.66108162654.81533768692-1.968243803427.913250813850.5134472182790.396352663264-0.687905783621-0.4819752052160.5525399119321.529278647410.00885965183020.176284617196-1.169591737960.58199416119-0.0765643065125-0.1182204337990.6508673940.1482058503650.9685658798381.8911227130143.244440556655.3650198151
46.87895259111-1.81547131088-5.441110730033.290747034490.7855115997539.735706585770.2962003534680.1987369345070.387601049029-0.2189617407730.1345491113260.0915896869785-0.573686402695-0.459372481778-0.3475654659480.416256426916-0.0634065517514-0.05404546496830.4153902682230.0578950205720.3976582108039.4822355854155.952355693247.6181448936
50.3165816502990.24031951089-0.09683559534483.55784161701-1.825879561193.782897601750.1060398558890.0709146332988-0.143779079802-0.408511152738-0.162687670416-0.1250399403830.3561955788960.3224628857350.06141981487760.440072190280.125677694302-0.003011863181730.4416370751970.02611140751080.37576005722623.658413895636.398770878757.5241695149
66.44926830118-0.5481119571310.5158940327048.58384822318-0.980561337898.296077725470.1206429381-0.6054501556380.03894052517010.9640229121930.002255078230790.5202330215320.388029322158-0.0171647891743-0.1064081460660.486711496166-0.04690221591560.02272838636350.3522266290330.0552517455230.38917971708119.929001843941.250528428673.5063181799
74.67379541097-1.877172944630.8711293069964.2410585317-1.029850500032.96337579794-0.0540878429656-0.775104346903-0.8394819521380.4560600238460.227475556330.4939250560610.112434879854-0.561540988898-0.1471229443140.40827180133-0.05263214495410.006736504278480.609644321350.174572718180.52403789645222.379645675816.507186797632.6181771543
85.70661587474-0.5007700062751.01014941813.91527545826-0.8021886729695.052587972530.214305600574-0.344464423118-0.3149241913980.0651007062909-0.356386131428-0.1570789900610.1744554711270.1019403098380.1894465144250.4960939132940.02627553617370.01329980988620.4261189347740.04595660951220.53094019564938.82562908298.87464944826.4373878929
92.75537619276-1.660712652230.7374700514544.26976760593-0.9426029338173.364157125980.379415690860.102088971606-0.63249759958-0.255485007697-0.2042455612450.4845158989330.484597067653-0.122237357453-0.1366799634310.409863209181-0.0199534600972-0.07201165252580.337891544650.03937623473320.44694257907720.641421663321.395113519218.2897375736
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 118 )
2X-RAY DIFFRACTION2chain 'A' and (resid 119 through 164 )
3X-RAY DIFFRACTION3chain 'A' and (resid 165 through 196 )
4X-RAY DIFFRACTION4chain 'A' and (resid 197 through 226 )
5X-RAY DIFFRACTION5chain 'A' and (resid 227 through 297 )
6X-RAY DIFFRACTION6chain 'A' and (resid 298 through 311 )
7X-RAY DIFFRACTION7chain 'B' and (resid 24 through 164 )
8X-RAY DIFFRACTION8chain 'B' and (resid 165 through 226 )
9X-RAY DIFFRACTION9chain 'B' and (resid 227 through 311 )

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