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- PDB-5m43: Crystal structure of Yvh1 phosphatase domain from Chaetomium ther... -

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Basic information

Entry
Database: PDB / ID: 5m43
TitleCrystal structure of Yvh1 phosphatase domain from Chaetomium thermophilum
ComponentsPutative uncharacterized protein
KeywordsRIBOSOME / phosphatase
Function / homology
Function and homology information


protein tyrosine/serine/threonine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity
Similarity search - Function
Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Protein-tyrosine-phosphatase
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.646 Å
AuthorsAhmed, Y.L. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: Protein Sci. / Year: 2017
Title: Interaction network of the ribosome assembly machinery from a eukaryotic thermophile.
Authors: Baler, J. / Ahmed, Y.L. / Kallas, M. / Kornprobst, M. / Calvino, F.R. / Gnadig, M. / Thoms, M. / Stier, G. / Ismail, S. / Kharde, S. / Castillo, N. / Griesel, S. / Bastuck, S. / Bradatsch, B. ...Authors: Baler, J. / Ahmed, Y.L. / Kallas, M. / Kornprobst, M. / Calvino, F.R. / Gnadig, M. / Thoms, M. / Stier, G. / Ismail, S. / Kharde, S. / Castillo, N. / Griesel, S. / Bastuck, S. / Bradatsch, B. / Thomson, E. / Flemming, D. / Sinning, I. / Hurt, E.
History
DepositionOct 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Jan 17, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9595
Polymers25,6511
Non-polymers3084
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint2 kcal/mol
Surface area8500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.758, 88.758, 53.079
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-583-

HOH

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Components

#1: Protein Putative uncharacterized protein


Mass: 25650.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495
Gene: CTHT_0021070 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0S3H6
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.04 Å3/Da / Density % sol: 39.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M LiNO3 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.646→45.55 Å / Num. obs: 25830 / % possible obs: 98.5 % / Redundancy: 8.6 % / Biso Wilson estimate: 20.09 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Net I/σ(I): 20.6
Reflection shellResolution: 1.65→1.67 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.62 / CC1/2: 0.916 / % possible all: 93.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.634
Highest resolutionLowest resolution
Rotation45.56 Å1.89 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.17data scaling
MOLREPphasing
PHENIX(1.10.1_2155: ???refinement
PDB_EXTRACT3.2data extraction
XSCALEdata scaling
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WRM

1wrm


Resolution: 1.646→44.379 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.66
RfactorNum. reflection% reflection
Rfree0.1868 1363 5.28 %
Rwork0.1631 --
obs0.1644 25797 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.39 Å2 / Biso mean: 33.5755 Å2 / Biso min: 14.55 Å2
Refinement stepCycle: final / Resolution: 1.646→44.379 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1335 0 20 222 1577
Biso mean--47.27 47.3 -
Num. residues----168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171419
X-RAY DIFFRACTIONf_angle_d1.3731917
X-RAY DIFFRACTIONf_chiral_restr0.103207
X-RAY DIFFRACTIONf_plane_restr0.01249
X-RAY DIFFRACTIONf_dihedral_angle_d15.822849
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6457-1.70450.24331460.20422298244495
1.7045-1.77280.20821330.19222387252098
1.7728-1.85350.2261190.17152399251898
1.8535-1.95120.16281400.15932403254398
1.9512-2.07340.16921100.15752438254898
2.0734-2.23350.17851300.14872436256698
2.2335-2.45830.20621410.1572436257799
2.4583-2.81390.18411570.1712456261399
2.8139-3.5450.16661420.16122525266799
3.545-44.39510.19331450.160926562801100
Refinement TLS params.Method: refined / Origin x: 22.4859 Å / Origin y: -0.3732 Å / Origin z: -9.4046 Å
111213212223313233
T0.1142 Å20.0046 Å20.0068 Å2-0.1175 Å2-0.0487 Å2--0.3369 Å2
L1.9943 °20.9866 °20.6377 °2-3.0795 °21.0163 °2--1.9839 °2
S-0.0457 Å °-0.082 Å °0.1212 Å °-0.102 Å °0.1164 Å °-0.2489 Å °-0.1513 Å °0.0045 Å °-0.0113 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 175
2X-RAY DIFFRACTION1allB1 - 2
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allS1 - 202
5X-RAY DIFFRACTION1allS203 - 222

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