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- PDB-2cwd: Crystal Structure of TT1001 protein from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 2cwd
TitleCrystal Structure of TT1001 protein from Thermus thermophilus HB8
Componentslow molecular weight phosphotyrosine protein phosphatase
KeywordsHYDROLASE / tyrosine phosphatase / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homology
Function and homology information


protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / metal ion binding
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 speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLokanath, N.K. / Terao, Y. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of TT1001 protein from Thermus thermophilus HB8
Authors: Lokanath, N.K. / Terao, Y. / Kunishima, N.
History
DepositionJun 20, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: low molecular weight phosphotyrosine protein phosphatase
B: low molecular weight phosphotyrosine protein phosphatase
C: low molecular weight phosphotyrosine protein phosphatase
D: low molecular weight phosphotyrosine protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9698
Polymers73,8724
Non-polymers974
Water7,170398
1
A: low molecular weight phosphotyrosine protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4922
Polymers18,4681
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: low molecular weight phosphotyrosine protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4922
Polymers18,4681
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: low molecular weight phosphotyrosine protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4922
Polymers18,4681
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: low molecular weight phosphotyrosine protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4922
Polymers18,4681
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.108, 31.293, 102.605
Angle α, β, γ (deg.)90.00, 98.70, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological assembly of this protein is monomer.

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Components

#1: Protein
low molecular weight phosphotyrosine protein phosphatase / protein-tyrosine phosphatase / TT1001 protein


Mass: 18467.926 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SJ34
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.1 Å3/Da / Density % sol: 41.9 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 6.5
Details: Magnesium acetate tetrahydrate, sodium cacodylate, PEG 8K, pH 6.5, microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 15, 2005
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 48911 / Num. obs: 48903 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 7.3
Reflection shellResolution: 1.9→1.97 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DG9

1dg9


Resolution: 1.9→38.04 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1585673.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2453 5 %RANDOM
Rwork0.227 ---
obs0.227 48903 98.5 %-
all-48911 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.0453 Å2 / ksol: 0.393821 e/Å3
Displacement parametersBiso mean: 32.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.88 Å20 Å2-9.48 Å2
2--2.16 Å20 Å2
3----5.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.9→38.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4889 0 4 398 5291
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.91
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.307 395 5 %
Rwork0.282 7448 -
obs--98.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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