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- PDB-3pr1: Crystal structure of apo Thermotoga maritima ribosome biogenesis ... -

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Basic information

Entry
Database: PDB / ID: 3pr1
TitleCrystal structure of apo Thermotoga maritima ribosome biogenesis GTP-binding protein EngB
ComponentsProbable GTP-binding protein engB
KeywordsHYDROLASE / Rossmann fold / GTP Binding / cell cycle
Function / homology
Function and homology information


division septum assembly / GTP binding / metal ion binding / cytosol
Similarity search - Function
GTP-binding protein, ribosome biogenesis, YsxC / EngB-type guanine nucleotide-binding (G) domain profile. / EngB-type guanine nucleotide-binding (G) domain / 50S ribosome-binding GTPase / GTP binding domain / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Probable GTP-binding protein EngB
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChan, K.H. / Wong, K.B.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structure of an essential GTPase, YsxC, from Thermotoga maritima
Authors: Chan, K.H. / Wong, K.B.
History
DepositionNov 29, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 23, 2011Group: Database references
Revision 1.3Nov 1, 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 / 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: Probable GTP-binding protein engB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5822
Polymers22,4871
Non-polymers951
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.717, 97.988, 54.847
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-262-

HOH

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Components

#1: Protein Probable GTP-binding protein engB


Mass: 22487.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: engB, TM_1466 / Plasmid: pRSETA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9X1H7
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.08 Å3/Da / Density % sol: 40.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M bis-tris pH 5.5, 2.0M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 1, 2007 / Details: VariMax HR optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→48.97 Å / Num. obs: 8326 / % possible obs: 96 % / Redundancy: 6.8 % / Biso Wilson estimate: 32.87 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 19.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CNSrefinement
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PQC

3pqc


Resolution: 2.3→28.403 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.85 / σ(F): 0.05 / Phase error: 24.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2567 390 4.8 %
Rwork0.2158 --
obs0.2177 8124 93.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.495 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.5912 Å20 Å2-0 Å2
2--16.444 Å20 Å2
3----15.8528 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.403 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1403 0 5 71 1479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061437
X-RAY DIFFRACTIONf_angle_d0.9511937
X-RAY DIFFRACTIONf_dihedral_angle_d16.694542
X-RAY DIFFRACTIONf_chiral_restr0.06217
X-RAY DIFFRACTIONf_plane_restr0.004238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.63260.30051430.21132577X-RAY DIFFRACTION96
2.6326-3.3160.25631170.19792689X-RAY DIFFRACTION98
3.316-28.40540.24221300.22072468X-RAY DIFFRACTION87

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