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- PDB-4lrq: Crystal structure of a Low Molecular Weight Phosphotyrosine phosp... -

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Basic information

Entry
Database: PDB / ID: 4lrq
TitleCrystal structure of a Low Molecular Weight Phosphotyrosine phosphatase from Vibrio choleraeO395
ComponentsPhosphotyrosine protein phosphatase
KeywordsHYDROLASE
Function / homology
Function and homology information


protein-tyrosine-phosphatase / protein tyrosine phosphatase activity
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 / Protein-tyrosine-phosphatase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsNath, S. / Banerjee, R. / Sen, U.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Atomic resolution crystal structure of VcLMWPTP-1 from Vibrio cholerae O395: insights into a novel mode of dimerization in the low molecular weight protein tyrosine phosphatase family.
Authors: Nath, S. / Banerjee, R. / Sen, U.
History
DepositionJul 20, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: Phosphotyrosine protein phosphatase
D: Phosphotyrosine protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,85616
Polymers69,2504
Non-polymers1,60612
Water7,062392
1
A: Phosphotyrosine protein phosphatase
C: Phosphotyrosine protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4288
Polymers34,6252
Non-polymers8036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-55 kcal/mol
Surface area14110 Å2
MethodPISA
2
B: Phosphotyrosine protein phosphatase
D: Phosphotyrosine protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4288
Polymers34,6252
Non-polymers8036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-58 kcal/mol
Surface area14030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.470, 87.470, 73.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Phosphotyrosine protein phosphatase


Mass: 17312.594 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: ATCC 39541 / Ogawa 395 / O395 / Gene: VC0395_A0559, VC395_1055 / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3
References: UniProt: A5F2Q3, UniProt: A0A0H3ALA8*PLUS, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2.4M ammonium sulfate, 0.1M citric acid pH 5.0, 2% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 7, 2011
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.284
11-K, -H, -L20.21
11K, H, -L30.216
11-h,-k,l40.29
ReflectionResolution: 1.45→23.89 Å / Num. obs: 110187 / % possible obs: 98.3 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.057
Reflection shellResolution: 1.45→1.488 Å / Mean I/σ(I) obs: 7.8 / Num. unique all: 110187 / % possible all: 98.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERMRphasing
REFMAC5.7.0029refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→23.41 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.214 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.014 / ESU R Free: 0.011 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.16063 5518 5 %RANDOM
Rwork0.15159 ---
obs0.15204 104633 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.062 Å2
Refine analyzeLuzzati coordinate error free: 0.011 Å
Refinement stepCycle: LAST / Resolution: 1.45→23.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4645 0 92 392 5129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0194820
X-RAY DIFFRACTIONr_bond_other_d0.0010.024602
X-RAY DIFFRACTIONr_angle_refined_deg0.9591.9886496
X-RAY DIFFRACTIONr_angle_other_deg0.939310633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4175593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.81824.537227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.92515850
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8271532
X-RAY DIFFRACTIONr_chiral_restr0.0990.2703
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215397
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021051
X-RAY DIFFRACTIONr_rigid_bond_restr2.90234820
X-RAY DIFFRACTIONr_sphericity_free3.5565121
X-RAY DIFFRACTIONr_sphericity_bonded5.0255014
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 432 -
Rwork0.399 7459 -
obs--95.15 %
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)
10.70.02930.04481.50240.16921.4318-0.00420.0020.0451-0.02490.01680.0432-0.013-0.0419-0.01260.02590.00980.00230.02370.00660.0375-10.5685-21.3912-19.0189
21.1383-0.4379-0.1641.05180.30871.28840.02240.02810.0009-0.0335-0.0110.05790.0005-0.0462-0.01140.0031-0.0059-0.00370.02240.00730.0263-30.55595.4556-7.0247
31.02110.52270.02851.7176-0.17941.27450.0436-0.11290.01560.2374-0.05070.075-0.0511-0.02240.00710.0447-0.01390.00790.0233-0.0010.0267-14.8796-43.44623.8284
41.3623-0.80980.11191.580.17171.4468-0.0841-0.1644-0.04660.18350.07270.028-0.0121-0.01440.01150.04650.00740.0030.0210.010.0336-13.5927-9.367816.0302
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 149
2X-RAY DIFFRACTION2B2 - 150
3X-RAY DIFFRACTION3C1 - 149
4X-RAY DIFFRACTION4D1 - 148

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