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- PDB-1wxq: Crystal Structure of GTP binding protein from Pyrococcus horikosh... -

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Basic information

Entry
Database: PDB / ID: 1wxq
TitleCrystal Structure of GTP binding protein from Pyrococcus horikoshii OT3
ComponentsGTP-binding proteinG protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / GTP-binding protein / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homology
Function and homology information


Helicase, Ruva Protein; domain 3 - #470 / Uncharacterised GTP-binding protein, C-terminal / Obg-like GTPase YGR210-like, G4 motif-containing domain / TGS domain / TGS / TGS-like / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. / Beta-grasp domain / 50S ribosome-binding GTPase ...Helicase, Ruva Protein; domain 3 - #470 / Uncharacterised GTP-binding protein, C-terminal / Obg-like GTPase YGR210-like, G4 motif-containing domain / TGS domain / TGS / TGS-like / 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 / Helicase, Ruva Protein; domain 3 / Ubiquitin-like (UB roll) / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
397aa long hypothetical GTP-binding protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsLokanath, N.K. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of GTP binding protein from Pyrococcus horikoshii OT3
Authors: Lokanath, N.K. / Kunishima, N.
History
DepositionJan 29, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTP-binding protein


Theoretical massNumber of molelcules
Total (without water)44,8461
Polymers44,8461
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.962, 142.999, 78.931
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Detailsbiological assembly is monomer

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Components

#1: Protein GTP-binding protein / G protein


Mass: 44846.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): 21-CodonPlus (DE3)-RIL / References: UniProt: O58261
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.4 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7.5
Details: PEG 4000, HEPES, Dioxane, pH 7.5, microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9791, 0.97942, 1.0
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 6, 2004 / Details: RH coated bent cylindrical mirror
RadiationMonochromator: Si111 double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.979421
311
ReflectionResolution: 2.6→30 Å / Num. all: 11882 / Num. obs: 11523 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 32.42 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.2
Reflection shellResolution: 2.6→2.69 Å / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.1.27refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→10 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.845 / SU B: 14.61 / SU ML: 0.326 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.927 / ESU R Free: 0.403 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29165 1293 10.1 %RANDOM
Rwork0.2659 ---
obs0.2659 11523 97.58 %-
all-11882 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.842 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--1.47 Å20 Å2
3----1.48 Å2
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2718 0 0 89 2807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222747
X-RAY DIFFRACTIONr_angle_refined_deg1.8111.9583716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7615339
X-RAY DIFFRACTIONr_chiral_restr0.1020.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022058
X-RAY DIFFRACTIONr_nbd_refined0.2920.21426
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2103
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3240.22
X-RAY DIFFRACTIONr_mcbond_it1.391.51708
X-RAY DIFFRACTIONr_mcangle_it2.45622753
X-RAY DIFFRACTIONr_scbond_it4.22531039
X-RAY DIFFRACTIONr_scangle_it6.2594.5963
LS refinement shellResolution: 2.6→2.663 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.277 98
Rwork0.271 800
Refinement TLS params.Method: refined / Origin x: 19.4837 Å / Origin y: 55.8748 Å / Origin z: 44.1178 Å
111213212223313233
T0.1244 Å20.0433 Å2-0.04 Å2-0.0436 Å20.0221 Å2--0.0582 Å2
L1.6366 °2-0.0282 °20.2831 °2-0.9338 °20.4818 °2--1.5719 °2
S0.0679 Å °-0.0014 Å °-0.0671 Å °0.0745 Å °0.021 Å °-0.0354 Å °0.3876 Å °0.1822 Å °-0.089 Å °

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