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- PDB-5z3m: Crystal structure of Low Molecular Weight Phosphotyrosine phospha... -

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Basic information

Entry
Database: PDB / ID: 5z3m
TitleCrystal structure of Low Molecular Weight Phosphotyrosine phosphatase (VcLMWPTP-2) from Vibrio choleraeO395
ComponentsPhosphotyrosine protein phosphatase
KeywordsHYDROLASE / Phosphatase / Ligand Bound
Function / homology
Function and homology information


protein tyrosine phosphatase activity / protein-tyrosine-phosphatase
Similarity search - Function
: / Protein-tyrosine phosphatase, low molecular weight / Phosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
protein-tyrosine-phosphatase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChatterjee, S. / Nath, S. / Sen, U.
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2019
Title: Vibrio cholerae LMWPTP-2 display unique surface charge and grooves around the active site: Indicative of distinctive substrate specificity and scope to design specific inhibitor.
Authors: Chatterjee, S. / Nath, S. / Ghosh, B. / Sen, U.
History
DepositionJan 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphotyrosine protein phosphatase
B: Phosphotyrosine protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,49341
Polymers37,6592
Non-polymers3,83439
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-22 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.912, 51.867, 83.896
Angle α, β, γ (deg.)90.00, 103.62, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-406-

HOH

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Components

#1: Protein Phosphotyrosine protein phosphatase


Mass: 18829.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395) (bacteria)
Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: VC0395_A0440 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0H3AM12, protein-tyrosine-phosphatase
#2: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 3.53 Å3/Da / Density % sol: 65.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: AMS, HEPES, GLYCEROL, MOPS, NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→19.402 Å / Num. obs: 31285 / % possible obs: 98.88 % / Redundancy: 2.53 % / Net I/σ(I): 8
Reflection shellResolution: 2.6→2.692 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LRQ

4lrq


Resolution: 2.6→19.402 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 34.62
RfactorNum. reflection% reflection
Rfree0.2883 1570 5.02 %
Rwork0.2518 --
obs0.2538 31285 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.402 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2424 0 246 257 2927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052673
X-RAY DIFFRACTIONf_angle_d1.0613550
X-RAY DIFFRACTIONf_dihedral_angle_d22.7641033
X-RAY DIFFRACTIONf_chiral_restr0.038376
X-RAY DIFFRACTIONf_plane_restr0.005437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.68380.34071470.2972671X-RAY DIFFRACTION100
2.6838-2.77950.35891460.28032749X-RAY DIFFRACTION100
2.7795-2.89040.28051400.28662770X-RAY DIFFRACTION100
2.8904-3.02150.3741300.27752658X-RAY DIFFRACTION98
3.0215-3.18010.38821240.29042699X-RAY DIFFRACTION98
3.1801-3.37840.27561320.25252709X-RAY DIFFRACTION99
3.3784-3.63770.28311340.23092739X-RAY DIFFRACTION99
3.6377-4.00080.22721350.22532755X-RAY DIFFRACTION99
4.0008-4.57310.28081680.21742661X-RAY DIFFRACTION99
4.5731-5.73690.27051760.24872674X-RAY DIFFRACTION99
5.7369-19.40290.26931380.25572630X-RAY DIFFRACTION97
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)
10.58190.5217-0.21841.50290.04431.3597-0.2013-0.044-0.2040.13440.0249-0.15350.29060.18570.03750.68490.07540.3007-0.0531-0.11810.152-26.35521.006713.7231
20.39960.2152-0.11220.6622-0.81951.0849-0.03740.0243-0.0852-0.1569-0.0083-0.04150.1811-0.01850.01980.7065-0.11080.20710.14280.02510.1571-40.2559-2.715413.8624
30.1654-0.5287-0.62363.90575.1256.7784-0.0853-0.0346-0.04940.2830.3434-0.16130.49340.7596-0.22770.60210.11720.28650.2147-0.0270.2925-30.7296-8.704214.9251
40.86071.50840.16313.4740.30690.07-0.053-0.0698-0.10760.2760.0401-0.00760.10080.0523-0.07480.64330.02830.26230.1834-0.04850.2512-32.059713.32318.8441
50.6828-0.0772-0.35160.97630.20340.2088-0.03450.1092-0.0606-0.1618-0.00880.0013-0.0510.0092-0.10030.6727-0.01220.15750.07460.0050.1158-30.832711.42827.2908
61.44080.7715-0.25663.1185-2.94363.7688-0.0083-0.02410.00320.0218-0.1539-0.1703-0.23490.20860.08130.59240.0310.19560.10310.03230.1537-29.391620.630110.8744
71.4868-0.32280.7622.68650.97271.6601-0.18880.2361-0.0106-0.0714-0.0538-0.08280.1851-0.00880.13890.822-0.07680.25710.1854-0.0010.2747-32.55463.44890.2576
81.0317-1.0186-1.09221.39131.25622.993-0.0368-0.1440.1660.08510.2432-0.2228-0.17720.3995-0.31920.61070.02450.36550.0912-0.12740.1389-24.6294-1.44453.8915
91.3193-0.2061-0.2740.95210.8314.0887-0.0548-0.0010.0731-0.03650.2138-0.1516-0.25260.5096-0.25380.5883-0.01110.28840.1563-0.11210.0832-32.8233-12.085131.6379
100.5013-0.1151-0.34881.26730.14380.74520.1236-0.09770.11620.12050.0406-0.057-0.06980.1058-0.13730.8723-0.04020.37520.1732-0.0280.2721-33.7187-13.304526.5335
110.0636-0.0502-0.03820.40350.62721.00370.036-0.03970.05050.00940.0010.056-0.0146-0.07650.07760.6382-0.07090.3470.1203-0.10410.2564-38.1126-3.086129.2958
121.3844-0.99830.7723.6749-1.17160.60480.0020.09620.3263-0.3192-0.0695-0.4402-0.0340.05880.03910.8057-0.0240.26970.1603-0.03260.4511-30.9566-24.033923.3
130.54941.3449-0.20064.0508-1.7332.10210.03960.24510.1734-0.05260.0467-0.0747-0.05640.0674-0.03470.7712-0.0010.24650.2006-0.00050.2749-33.2977-21.959934.7112
140.4166-0.5422-0.03312.8362-0.40940.1925-0.0363-0.00360.00780.1886-0.035-0.14770.10950.03490.0830.7368-0.00570.2830.06960.080.1993-33.6065-27.729234.6298
152.3446-1.0902-0.11443.17480.12522.2810.0812-0.19430.0330.01170.21870.0978-0.437-0.4787-0.2761.04250.03250.4210.320.03320.4393-45.2469-15.289739.7967
160.99280.3094-0.30613.1637-0.73812.5662-0.0186-0.07610.01680.06940.0075-0.18040.52490.1180.16061.0166-0.04340.32470.169-0.02460.2665-34.7197-10.639140.6209
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 61 )
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 71 )
4X-RAY DIFFRACTION4chain 'A' and (resid 72 through 82 )
5X-RAY DIFFRACTION5chain 'A' and (resid 83 through 96 )
6X-RAY DIFFRACTION6chain 'A' and (resid 97 through 108 )
7X-RAY DIFFRACTION7chain 'A' and (resid 109 through 130 )
8X-RAY DIFFRACTION8chain 'A' and (resid 131 through 157 )
9X-RAY DIFFRACTION9chain 'B' and (resid 5 through 32 )
10X-RAY DIFFRACTION10chain 'B' and (resid 33 through 54 )
11X-RAY DIFFRACTION11chain 'B' and (resid 55 through 71 )
12X-RAY DIFFRACTION12chain 'B' and (resid 72 through 82 )
13X-RAY DIFFRACTION13chain 'B' and (resid 83 through 91 )
14X-RAY DIFFRACTION14chain 'B' and (resid 92 through 115 )
15X-RAY DIFFRACTION15chain 'B' and (resid 116 through 130 )
16X-RAY DIFFRACTION16chain 'B' and (resid 131 through 156 )

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