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- PDB-1wf3: Crystal structure of GTP-binding protein TT1341 from Thermus ther... -

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Basic information

Entry
Database: PDB / ID: 1wf3
TitleCrystal structure of GTP-binding protein TT1341 from Thermus thermophilus HB8
ComponentsGTP-binding proteinG protein
KeywordsHYDROLASE / GTP-binding protein / GTPase / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


ribosomal small subunit binding / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / GTPase activity / GTP binding / plasma membrane / cytoplasm
Similarity search - Function
GTP-binding protein Era / Era-type guanine nucleotide-binding (G) domain / Era-type guanine nucleotide-binding (G) domain profile. / K homology (KH) domain / 50S ribosome-binding GTPase / GTP binding domain / GMP Synthetase; Chain A, domain 3 / K Homology domain, type 2 / KH domain / K homology domain superfamily, prokaryotic type ...GTP-binding protein Era / Era-type guanine nucleotide-binding (G) domain / Era-type guanine nucleotide-binding (G) domain profile. / K homology (KH) domain / 50S ribosome-binding GTPase / GTP binding domain / GMP Synthetase; Chain A, domain 3 / K Homology domain, type 2 / KH domain / K homology domain superfamily, prokaryotic type / Type-2 KH domain profile. / K homology domain-like, alpha/beta / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase Era
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.88 Å
AuthorsKawazoe, M. / Hori-Takemoto, C. / Kaminishi, T. / Sekine, S. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of GTP-binding protein TT1341 from Thermus thermophilus HB8
Authors: Kawazoe, M. / Hori-Takemoto, C. / Kaminishi, T. / Sekine, S. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 25, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5875
Polymers33,8561
Non-polymers7314
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.634, 68.634, 86.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein GTP-binding protein / G protein


Mass: 33856.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TT1341 / Plasmid: pET11b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SM23
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 178 / 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 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M Bicin, 5% v/v Glycerol, 10% w/v PEG8000, 4% v/v Dioxane, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONSPring-8 BL44B211
ROTATING ANODERIGAKU22.29
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 25, 2004
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
22.291
ReflectionResolution: 1.88→31.9 Å / Num. obs: 32500 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 7.53932 % / Biso Wilson estimate: 28.3 Å2
Reflection shellResolution: 1.88→1.95 Å / Rsym value: 0.66 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.88→31.89 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1227309.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1609 5 %RANDOM
Rwork0.2 ---
obs0.2 32440 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.1152 Å2 / ksol: 0.375803 e/Å3
Displacement parametersBiso mean: 41.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.21 Å20 Å20 Å2
2--3.21 Å20 Å2
3----6.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.88→31.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2353 0 45 178 2576
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it3.162.5
LS refinement shellResolution: 1.88→2 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.275 327 6 %
Rwork0.244 5093 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2GNP_XPLOR_PAR.TXTGOL_CNS_TOP.TXT
X-RAY DIFFRACTION3ION.PARAMWATER.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION5GOL_CNS_PAR.TXTGNP_XPLOR_TOP.TXT

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