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- PDB-4erc: Structure of VHZ bound to metavanadate -

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Basic information

Entry
Database: PDB / ID: 4erc
TitleStructure of VHZ bound to metavanadate
ComponentsDual specificity protein phosphatase 23
KeywordsHYDROLASE / Alpha Beta / Phosphatase(hydrolase)
Function / homology
Function and homology information


protein tyrosine/serine/threonine phosphatase activity / dephosphorylation / myosin phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / cilium assembly / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Swiss Army Knife protein, DSP-PTPase phosphatase domain / : / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif ...Swiss Army Knife protein, DSP-PTPase phosphatase domain / : / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
oxido(dioxo)vanadium / Dual specificity protein phosphatase 23
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsVyacheslav, K. / Alvan, C.H. / Sean, J.J.
CitationJournal: Biochemistry / Year: 2012
Title: New Aspects of the Phosphatase VHZ Revealed by a High-Resolution Structure with Vanadate and Substrate Screening.
Authors: Kuznetsov, V.I. / Hengge, A.C. / Johnson, S.J.
History
DepositionApr 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Feb 28, 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

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Assembly

Deposited unit
A: Dual specificity protein phosphatase 23
B: Dual specificity protein phosphatase 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4184
Polymers33,2202
Non-polymers1982
Water7,909439
1
A: Dual specificity protein phosphatase 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7092
Polymers16,6101
Non-polymers991
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dual specificity protein phosphatase 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7092
Polymers16,6101
Non-polymers991
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.992, 79.970, 99.718
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dual specificity protein phosphatase 23 / Low molecular mass dual specificity phosphatase 3 / LDP-3 / VH1-like phosphatase Z


Mass: 16610.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP23, LDP3, VHZ / Plasmid: pET45b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon+ (DE3)-RIL
References: UniProt: Q9BVJ7, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#2: Chemical ChemComp-VN4 / oxido(dioxo)vanadium


Mass: 98.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 1.98 Å3/Da / Density % sol: 37.88 %
Crystal growTemperature: 298 K / pH: 7.5
Details: VHZ 20 mg/mL in the crystallization buffer was mixed with 50 mM solution of sodium vanadate (final vanadate concentration 10mM One uL of protein-vanadate complex was mixed with an equal ...Details: VHZ 20 mg/mL in the crystallization buffer was mixed with 50 mM solution of sodium vanadate (final vanadate concentration 10mM One uL of protein-vanadate complex was mixed with an equal volume of well solution containing 150 mM L-Malate, pH 7.0 and PEG3350 (15-20 % v/w), VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 30, 2010 / Details: MIRRORS
RadiationMonochromator: SI 111 DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 94449 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 31.3
Reflection shellResolution: 1.15→1.19 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 3.8 / % possible all: 99.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
X-PLORmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→31.32 Å / SU ML: 0.09 / σ(F): 0 / Phase error: 12.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.145 1941 2.13 %
Rwork0.128 --
obs0.129 91098 95.9 %
all-94449 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.89 Å2 / ksol: 0.42 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1209 Å2-0 Å20 Å2
2---1.3788 Å20 Å2
3---0.2579 Å2
Refinement stepCycle: LAST / Resolution: 1.15→31.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2338 0 8 439 2785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082478
X-RAY DIFFRACTIONf_angle_d1.2453377
X-RAY DIFFRACTIONf_dihedral_angle_d12.691948
X-RAY DIFFRACTIONf_chiral_restr0.067362
X-RAY DIFFRACTIONf_plane_restr0.007456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1488-1.17750.21331220.1655761X-RAY DIFFRACTION87
1.1775-1.20940.15991310.13595976X-RAY DIFFRACTION92
1.2094-1.2450.16341310.12086057X-RAY DIFFRACTION93
1.245-1.28510.15811350.11246180X-RAY DIFFRACTION94
1.2851-1.33110.131370.10676291X-RAY DIFFRACTION95
1.3311-1.38440.14411380.10366304X-RAY DIFFRACTION96
1.3844-1.44740.13961410.10346369X-RAY DIFFRACTION97
1.4474-1.52370.14451380.10336435X-RAY DIFFRACTION98
1.5237-1.61910.12741410.09956483X-RAY DIFFRACTION98
1.6191-1.74410.15021440.10436545X-RAY DIFFRACTION99
1.7441-1.91960.12561450.11656543X-RAY DIFFRACTION98
1.9196-2.19740.13141450.11386691X-RAY DIFFRACTION100
2.1974-2.76820.14411460.12816722X-RAY DIFFRACTION100
2.7682-31.33380.1511470.16096800X-RAY DIFFRACTION97

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