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- PDB-8hgw: Crystal structure of MehpH in complex with MBP -

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Basic information

Entry
Database: PDB / ID: 8hgw
TitleCrystal structure of MehpH in complex with MBP
ComponentsMonoalkyl phthalate hydrolase
KeywordsHYDROLASE
Function / homology: / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / membrane / 1-BUTANOL / PHTHALIC ACID / Monoethylhexylphthalate hydrolase
Function and homology information
Biological speciesGordonia sp. P8219 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.80001173333 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 / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity_src_gen / struct_ncs_dom_lim
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Monoalkyl phthalate hydrolase
B: Monoalkyl phthalate hydrolase
C: Monoalkyl phthalate hydrolase
D: Monoalkyl phthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,7329
Polymers125,9944
Non-polymers7395
Water00
1
A: Monoalkyl phthalate hydrolase
D: Monoalkyl phthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4035
Polymers62,9972
Non-polymers4063
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint7 kcal/mol
Surface area21130 Å2
MethodPISA
2
B: Monoalkyl phthalate hydrolase
hetero molecules

C: Monoalkyl phthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3294
Polymers62,9972
Non-polymers3322
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_665x+1,y+1,z1
Buried area2630 Å2
ΔGint5 kcal/mol
Surface area20990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.95, 48.95, 306.325
Angle α, β, γ (deg.)90.0, 93.7297, 90.0
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEPROPROchain 'A'AA24 - 1742 - 152
12SERSERLEULEUchain 'A'AA177 - 311155 - 289
21PHEPHEPROPROchain 'B'BB24 - 1742 - 152
22SERSERLEULEUchain 'B'BB177 - 311155 - 289
31PHEPHEPROPROchain 'C'CC24 - 1742 - 152
32SERSERLEULEUchain 'C'CC177 - 311155 - 289
41PHEPHEPROPROchain 'D'DD24 - 1742 - 152
42SERSERLEULEUchain 'D'DD177 - 311155 - 289

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Components

#1: Protein
Monoalkyl phthalate hydrolase


Mass: 31498.416 Da / Num. of mol.: 4
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: Chemical ChemComp-1BO / 1-BUTANOL / BUTAN-1-OL


Mass: 74.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PHT / PHTHALIC ACID


Mass: 166.131 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H6O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 100 mM Bis-Tris, pH 6.2, 22% (w/v) PEG 3350 and 250 mM MgCl2.6H2O

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 0.97914 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.8→46.38 Å / Num. obs: 32749 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 43.9043707499 Å2 / CC1/2: 0.95 / Net I/σ(I): 8.2
Reflection shellResolution: 2.8→2.97 Å / Num. unique obs: 28590 / CC1/2: 0.826

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2

Resolution: 2.80001173333→44.1224888313 Å / SU ML: 0.422159411572 / Cross valid method: FREE R-VALUE / σ(F): 1.34755448172 / Phase error: 28.8454925669
RfactorNum. reflection% reflection
Rfree0.259565441725 1445 5.05421476041 %
Rwork0.227606451094 27145 -
obs0.229228396146 28590 99.769681742 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.4561602992 Å2
Refinement stepCycle: LAST / Resolution: 2.80001173333→44.1224888313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8669 0 5 0 8674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00483703909088891
X-RAY DIFFRACTIONf_angle_d0.99828741845612133
X-RAY DIFFRACTIONf_chiral_restr0.03976382369961358
X-RAY DIFFRACTIONf_plane_restr0.008146845191681587
X-RAY DIFFRACTIONf_dihedral_angle_d15.73295983353058
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.801-2.90010.4111731556391390.3458499910932702X-RAY DIFFRACTION99.8594024605
2.9001-3.01620.3552688316541450.313043936072671X-RAY DIFFRACTION99.7520368402
3.0162-3.15340.3244739666271380.2914816292212685X-RAY DIFFRACTION99.8938428875
3.1534-3.31960.3234175131141280.2716802585692706X-RAY DIFFRACTION99.7536078845
3.3196-3.52750.2971237647031430.2548691166322718X-RAY DIFFRACTION99.8603839442
3.5275-3.79970.2555796173011480.2217551569652692X-RAY DIFFRACTION99.8944776644
3.7997-4.18180.2285881882611440.2134555435562696X-RAY DIFFRACTION99.9648011264
4.1818-4.78630.2148913895481370.1810244356012750X-RAY DIFFRACTION99.7581202488
4.7863-6.02780.2160540505191530.2075227298362724X-RAY DIFFRACTION99.8265093685
6.0278-100.2203908178511700.1803983703752801X-RAY DIFFRACTION99.1655540721
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)
12.40352841906-0.0879662863234-0.4971173901821.335113609280.5393818985892.709344647830.0215271438826-0.5586961842540.04108045358850.290996942761-0.0934024826995-0.09738683526440.2171750226720.41644089680.06782686860810.295614922834-0.114606253452-0.06252693996710.6457241517930.07579669652090.3117053739292.785813181151.94859614017-45.6246318574
26.14174369494-0.0873012023214-0.1517751048522.62351720109-0.1724235633134.59516195498-0.06521110696010.648081084370.8188972580280.1438956977830.0751198482934-0.771020603701-0.05004286677020.519993130619-0.07262375660310.300079279717-0.0949866390432-0.0600697010450.5365110400750.02143604871310.3974446205147.193798926332.35840453828-67.7861636043
33.05810842069-1.072248499320.1633285657630.439069969495-0.07667322456992.068110875830.03813604277060.16402093104-0.09011618630790.0473005098596-0.116398118298-0.048267261756-0.04820129147370.2222460880860.08735231479530.245358800407-0.1201520574190.001802721964730.3157259941110.0026747217660.310471194037-3.57654465665-0.23097094463-54.0148953677
41.480235921610.1077318921390.1362877046791.302061867770.5954373231691.7401047633-0.000352943712168-0.05138460054580.0162017412203-0.07233579114440.0448751339836-0.02386517500650.610764221674-0.457562160109-0.1165988898080.471907871022-0.322679655262-0.07502270130241.246395437140.04865519404780.31728164011913.968075301514.7741651882-20.2041802295
51.133151922190.86580871107-0.1637700572450.679008687176-0.08402847324790.1535744480030.341886854240.5912012994190.984039264902-0.1684021766310.369002781530.489837337823-0.259639723291-0.284970153048-0.1870762073770.2751651847190.00395568809180.2094762020611.813404000980.3312649925390.7072851704227.405741245930.9757945562-9.18660195801
61.464161952270.647918727395-0.7799358864520.947570326410.1291283122610.904262393192-0.145891150057-0.334969057377-0.0148727599315-0.03742206999860.284632789927-0.07785534361840.276118083943-0.406676648312-0.06150268204870.304332490618-0.2074171490030.006384888149481.266092822840.01255695684280.3541147734422.578915261619.218735798-12.7029655039
73.364905815570.160686240104-1.555137304552.49169688975-0.9452434049113.214824794310.35266333762-0.03783715929450.1109249337790.201903742973-0.269008446566-0.136031279179-0.6407571677520.0686369778447-0.05570649856070.407275346419-0.1951360609410.02208926342860.7807343818430.03551469360270.328323569535-26.7494286765-6.96145432279-25.7493831182
80.3325332577280.5457395785040.8031505125664.77977312385-0.00877146974922.44071457382-0.359865330776-0.380458513604-0.715402604441-0.376885338737-0.07272027975970.172501162230.3136554253330.4277169408040.3073826542350.341422454469-0.04967832240440.02286069369741.368437656470.2735708356640.805292613478-17.8050451253-26.207241125-20.0410465132
92.822403584660.37423555087-0.003825942656151.59708071947-1.240118905591.080581021790.0381173532849-0.253934544142-0.2149936104030.195583111156-0.230124366795-0.132312640592-0.120016896640.5098292456120.1095025503160.341963560953-0.197796953630.01909936769190.987482562148-0.02862886974720.361823980701-29.2526760477-14.6944656728-18.0201205305
101.22461292747-0.0421991705556-0.2924446814642.1701847576-0.507140790832.902115620080.0313343939296-0.04503347762280.4589086061510.2217712057110.1835645490480.0741654308027-0.863336398882-0.27687914935-0.2352486885940.4856582256570.07609093160040.0468336260630.375670483389-0.03257184379550.524030259158-36.176481103226.0296882016-59.6487040623
114.519477231290.680765318392-1.149982525722.55217704289-0.9231488359973.44656157357-0.1142702772470.227177843514-0.1372856382530.124820359860.1226357907420.175171052138-0.206425869356-0.551625137898-0.009252281970990.221544486770.0678109635916-0.03950007925870.4266236205560.01217411967350.336199892763-35.727555220411.6688921276-59.1109093757
122.86465519655-0.2594787604051.058937186391.84760654628-0.6932964257122.307067270810.0416127589990.1429004165680.096624069180.160317650705-0.01468522558880.185545131248-0.179374499652-0.3468406448280.01323099733110.272076112683-0.02173897039020.002695136028170.34986262188-0.03599980574950.287397454651-31.536645840612.4626556831-61.2733447617
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 163 )
2X-RAY DIFFRACTION2chain 'A' and (resid 164 through 196 )
3X-RAY DIFFRACTION3chain 'A' and (resid 197 through 311 )
4X-RAY DIFFRACTION4chain 'B' and (resid 24 through 163 )
5X-RAY DIFFRACTION5chain 'B' and (resid 164 through 207 )
6X-RAY DIFFRACTION6chain 'B' and (resid 208 through 311 )
7X-RAY DIFFRACTION7chain 'C' and (resid 24 through 161 )
8X-RAY DIFFRACTION8chain 'C' and (resid 162 through 196 )
9X-RAY DIFFRACTION9chain 'C' and (resid 197 through 311 )
10X-RAY DIFFRACTION10chain 'D' and (resid 24 through 118 )
11X-RAY DIFFRACTION11chain 'D' and (resid 119 through 196 )
12X-RAY DIFFRACTION12chain 'D' and (resid 197 through 311 )

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