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- PDB-2dwq: Thermus thermophilus YchF GTP-binding protein -

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Basic information

Entry
Database: PDB / ID: 2dwq
TitleThermus thermophilus YchF GTP-binding protein
ComponentsGTP-binding protein
KeywordsHYDROLASE / GTP-binding / signal transduction / TGS domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


ribosomal large subunit binding / GTP binding / ATP hydrolysis activity / ATP binding
Similarity search - Function
Obg-related GTPase Ych/YyaF, coiled-coil domain / Ribosome-binding ATPase YchF/Obg-like ATPase 1 / YchF, C-terminal domain / TGS-like domain superfamily / YchF, N-terminal / Protein of unknown function (DUF933) / TGS-like / TGS domain profile. / TGS / OBG-type guanine nucleotide-binding (G) domain ...Obg-related GTPase Ych/YyaF, coiled-coil domain / Ribosome-binding ATPase YchF/Obg-like ATPase 1 / YchF, C-terminal domain / TGS-like domain superfamily / YchF, N-terminal / Protein of unknown function (DUF933) / TGS-like / TGS domain profile. / TGS / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. / Beta-grasp domain / 50S ribosome-binding GTPase / GTP binding domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / DNA polymerase; domain 1 / P-loop containing nucleotide triphosphate hydrolases / Roll / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ribosome-binding ATPase YchF
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsKukimoto-Niino, M. / Murayama, K. / Shorouzu, M. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Thermus thermophilus YchF GTP-binding protein
Authors: Kukimoto-Niino, M. / Murayama, K. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S.
History
DepositionAug 16, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2007Provider: 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 / 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: GTP-binding protein
B: GTP-binding protein


Theoretical massNumber of molelcules
Total (without water)81,1312
Polymers81,1312
Non-polymers00
Water55831
1
A: GTP-binding protein


Theoretical massNumber of molelcules
Total (without water)40,5651
Polymers40,5651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTP-binding protein


Theoretical massNumber of molelcules
Total (without water)40,5651
Polymers40,5651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.940, 54.357, 92.585
Angle α, β, γ (deg.)80.11, 76.46, 73.12
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a monomer.

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Components

#1: Protein GTP-binding protein


Mass: 40565.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SJ29
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 3.03 Å3/Da / Density % sol: 59.47 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.01M Cobaltous Chloride, 0.1M Sodium Acetate, 1M 1,6 Hexanediol, 4% Acetone, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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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 24, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 18991 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 1.83013 % / Biso Wilson estimate: -0.4 Å2 / Rsym value: 0.12 / Net I/σ(I): 6.0465
Reflection shellResolution: 2.9→3 Å / Mean I/σ(I) obs: 2.41909 / Rsym value: 0.164 / % possible all: 83.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DBY

2dby


Resolution: 2.95→37.04 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 716396.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1872 9.9 %RANDOM
Rwork0.208 ---
obs0.208 18991 94.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.2323 Å2 / ksol: 0.286933 e/Å3
Displacement parametersBiso mean: 60.7 Å2
Baniso -1Baniso -2Baniso -3
1-13.38 Å2-20.79 Å27.79 Å2
2--6.03 Å2-2.18 Å2
3----19.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.95→37.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5379 0 0 31 5410
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d1.43
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.405 206 10.7 %
Rwork0.38 1718 -
obs--54.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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