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- PDB-8gz4: Crystal structure of MPXV phosphatase -

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Basic information

Entry
Database: PDB / ID: 8gz4
TitleCrystal structure of MPXV phosphatase
ComponentsDual specificity protein phosphatase H1
KeywordsVIRAL PROTEIN / inhibitor / dimer / phosphate
Function / homology
Function and homology information


protein tyrosine/serine/threonine phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / protein dephosphorylation / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / cytoplasm
Similarity search - Function
Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain ...Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like
Similarity search - Domain/homology
PHOSPHATE ION / Dual specificity protein phosphatase H1
Similarity search - Component
Biological speciesMonkeypox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 Å
AuthorsYang, H.T. / Wang, W. / Huang, H.J. / Ji, X.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81902063 China
CitationJournal: Protein Cell / Year: 2023
Title: Crystal structure of monkeypox H1 phosphatase, an antiviral drug target.
Authors: Cui, W. / Huang, H. / Duan, Y. / Luo, Z. / Wang, H. / Zhang, T. / Nguyen, H.C. / Shen, W. / Su, D. / Li, X. / Ji, X. / Yang, H. / Wang, W.
History
DepositionSep 25, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Dec 6, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity protein phosphatase H1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8502
Polymers19,7551
Non-polymers951
Water1,78399
1
A: Dual specificity protein phosphatase H1
hetero molecules

A: Dual specificity protein phosphatase H1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7004
Polymers39,5102
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_444-y-1/2,-x-1/2,-z-1/21
Buried area2540 Å2
ΔGint-43 kcal/mol
Surface area16040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.480, 62.480, 170.494
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-387-

HOH

21A-395-

HOH

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Components

#1: Protein Dual specificity protein phosphatase H1 / H1L / MPXV-COP-085 / MPXV-SL-085 / MPXV-WRAIR085 / MPXVgp091 / Tyr-ser protein phosphatase / ...H1L / MPXV-COP-085 / MPXV-SL-085 / MPXV-WRAIR085 / MPXVgp091 / Tyr-ser protein phosphatase / Tyr/Ser phosphatase / IFN-gamma inhibitor / Tyr/ser protein phosphatase


Mass: 19754.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus
Gene: H1L, MPXV-CAM1990_02-083, MPXV-Congo_8-084, MPXV-COP-085, MPXV-GAB1988_001-084, MPXV-Ikubi-083, MPXV-M2940_FCT-089, MPXV-M2957_Lagos-089, MPXV-M3021_Delta-089, MPXV-M5312_HM12_Rivers-089, MPXV- ...Gene: H1L, MPXV-CAM1990_02-083, MPXV-Congo_8-084, MPXV-COP-085, MPXV-GAB1988_001-084, MPXV-Ikubi-083, MPXV-M2940_FCT-089, MPXV-M2957_Lagos-089, MPXV-M3021_Delta-089, MPXV-M5312_HM12_Rivers-089, MPXV-M5320_M15_Bayelsa-082, MPXV-Nig_SEV71_2_82-084, MPXV-PCH-086, MPXV-Singapore-089, MPXV-SL-085, MPXV-UK_P1-089, MPXV-UK_P2-089, MPXV-UK_P3-089, MPXV-USA2003_099_GR-089, MPXV-USA2003_206_DM-089, MPXV-USA2003_223_RS-089, MPXV-UTC-080, MPXV-W_Nigeria-084, MPXV-WRAIR085, MPXV297957_080, MPXV298464_071, MPXV_DRC_Yandongi_092, MPXV_LIB1970_184_096, MPXV_RCG2003_358_096, MPXV_ROC_2010_035, MPXV_SUD2005_01_092, MPXV_USA2003_039_096, MPXV_USA2003_044_096, MPXV_ZAI1979_005_096, MPXVgp091, PDLMKLCO_00094
Production host: Escherichia coli (E. coli)
References: UniProt: Q5IXT4, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: BIS-TRIS, PEG 3350, Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9777 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 1.8→30.675 Å / Num. obs: 29840 / % possible obs: 99.9 % / Redundancy: 16.089 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.076 / Χ2: 0.949 / Net I/σ(I): 25.92
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.8516.4710.6624.7419370118111760.9490.68399.6
1.85-1.916.7130.5886.118919113311320.9660.60699.9
1.9-1.9515.1530.5167.0816729110611040.9660.53499.8
1.95-2.0117.3840.3369.6418827108310830.9860.346100
2.01-2.0816.3450.27712.5717031104210420.9960.287100
2.08-2.1517.2860.2115.2517493101210120.9950.216100
2.15-2.2416.7990.16818.41163969769760.9940.174100
2.24-2.3315.6850.14621.33148699499480.9970.15199.9
2.33-2.4317.2970.11525.48154988968960.9980.118100
2.43-2.5516.0730.10228.26140808768760.9970.105100
2.55-2.6916.6020.09232.11138968378370.9980.095100
2.69-2.8516.8740.08236.6133817937930.9980.084100
2.85-3.0516.2480.06642.12120077397390.9990.068100
3.05-3.2914.8550.05744.17104587047040.9990.059100
3.29-3.615.0740.04951.795876366360.9990.051100
3.6-4.0313.780.04752.7882545995990.9970.049100
4.03-4.6515.4630.0425981185255250.9990.044100
4.65-5.713.9110.03956.2364134624610.9990.04199.8
5.7-8.0614.2350.03954.9452103663660.9990.041100
8.06-30.67513.2360.03159.3629782322250.9990.03397

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3cm3

3cm3


Resolution: 1.802→30.675 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1965 2987 10.01 %
Rwork0.1724 26853 -
obs0.1748 29840 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.02 Å2 / Biso mean: 29.2832 Å2 / Biso min: 10.91 Å2
Refinement stepCycle: final / Resolution: 1.802→30.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1356 0 5 99 1460
Biso mean--26.63 36.9 -
Num. residues----170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081423
X-RAY DIFFRACTIONf_angle_d0.931936
X-RAY DIFFRACTIONf_chiral_restr0.054219
X-RAY DIFFRACTIONf_plane_restr0.006245
X-RAY DIFFRACTIONf_dihedral_angle_d11.72874
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.802-1.83120.27971430.2334127399
1.8312-1.86280.2651440.21821276100
1.8628-1.89660.29081380.22191282100
1.8966-1.93310.24611380.23761268100
1.9331-1.97260.24991420.19731298100
1.9726-2.01540.22851440.18051269100
2.0154-2.06230.21591360.15961272100
2.0623-2.11390.19141440.17571282100
2.1139-2.1710.21321420.16461288100
2.171-2.23490.21761440.16021270100
2.2349-2.3070.18531470.16561251100
2.307-2.38940.20611470.16041307100
2.3894-2.4850.18991450.16421249100
2.485-2.59810.19711460.18011307100
2.5981-2.7350.23381350.18411267100
2.735-2.90620.21921350.17411289100
2.9062-3.13040.20571410.18491272100
3.1304-3.44510.17421440.17461277100
3.4451-3.94270.16811420.15751293100
3.9427-4.96390.17091420.14811270100
4.9639-30.6750.17711480.17571293100
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)
10.58870.415-0.3160.5349-0.10420.56880.01610.05470.16870.1327-0.0964-0.1118-0.2280.3158-0.00720.2123-0.01120.00890.18290.00620.2318-2.8469-18.2778-39.109
22.8345-0.268-0.31431.9786-0.19943.46010.0707-0.53830.05080.18860.0754-0.0193-0.32790.0682-0.0630.1710.00280.01280.2601-0.02730.1325-10.2424-22.8227-14.3749
32.39840.14140.44571.3632-0.39792.86390.0320.05480.15790.01720.03160.0316-0.2662-0.1813-0.07590.16820.03860.02680.1495-0.00060.1864-13.8319-20.0431-30.817
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 25 )A2 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 115 )A26 - 115
3X-RAY DIFFRACTION3chain 'A' and (resid 116 through 171 )A116 - 171

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