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- PDB-3kxl: crystal structure of SsGBP mutation variant G235S -

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Basic information

Entry
Database: PDB / ID: 3kxl
Titlecrystal structure of SsGBP mutation variant G235S
ComponentsGTP-binding protein (HflX)
KeywordsNUCLEOTIDE BINDING PROTEIN / SsGBP / HflX / GTPase / GTP hydrolysis
Function / homology
Function and homology information


ribosome binding / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3070 / GTPase HflX, N-terminal domain / GTPase HflX / GTPase HflX, N-terminal / HflX-type guanine nucleotide-binding (G) domain / GTP-binding protein, middle domain / GTPase HflX, N-terminal domain superfamily / GTP-binding GTPase N-terminal / GTP-binding GTPase Middle Region / HflX-type guanine nucleotide-binding (G) domain profile. ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3070 / GTPase HflX, N-terminal domain / GTPase HflX / GTPase HflX, N-terminal / HflX-type guanine nucleotide-binding (G) domain / GTP-binding protein, middle domain / GTPase HflX, N-terminal domain superfamily / GTP-binding GTPase N-terminal / GTP-binding GTPase Middle Region / HflX-type guanine nucleotide-binding (G) domain profile. / 50S ribosome-binding GTPase / GTP binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / 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
THIOCYANATE ION / GTPase HflX
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsHuang, B. / Li, X. / Zhang, X.C. / Rao, Z.
CitationJournal: J.Biochem. / Year: 2010
Title: Functional study on GTP hydrolysis by the GTP binding protein from Sulfolobus solfataricus, a member of the HflX family.
Authors: Huang, B. / Wu, H. / Hao, N. / Blombach, F. / van der Oost, J. / Li, X. / Zhang, X.C. / Rao, Z.
History
DepositionDec 3, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 10, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTP-binding protein (HflX)
B: GTP-binding protein (HflX)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4473
Polymers83,3892
Non-polymers581
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-14 kcal/mol
Surface area28340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.608, 71.136, 97.112
Angle α, β, γ (deg.)90.00, 96.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GTP-binding protein (HflX)


Mass: 41694.621 Da / Num. of mol.: 2 / Mutation: G235S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: hflX, SSO0269 / Plasmid: pET 24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q980M3
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.29 Å3/Da / Density % sol: 46.2 % / Mosaicity: 1.107 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 12% (w/v) PEG 3350, 0.16M sodium thiocyanate, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorDate: Oct 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 26261 / % possible obs: 99.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.069 / Χ2: 1.102 / Net I/σ(I): 8.7
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 3.8 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QTF

2qtf


Resolution: 2.5→38.372 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.761 / SU ML: 0.31 / σ(F): 0.14 / Phase error: 29.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.264 1277 5.1 %
Rwork0.24 --
obs0.241 25060 95.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.496 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 112.59 Å2 / Biso mean: 51.062 Å2 / Biso min: 19.91 Å2
Baniso -1Baniso -2Baniso -3
1-2.3667 Å20 Å2-10.5977 Å2
2---7.2562 Å20 Å2
3---4.8894 Å2
Refinement stepCycle: LAST / Resolution: 2.5→38.372 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4703 0 3 66 4772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024778
X-RAY DIFFRACTIONf_angle_d0.4056443
X-RAY DIFFRACTIONf_dihedral_angle_d10.8161816
X-RAY DIFFRACTIONf_chiral_restr0.027775
X-RAY DIFFRACTIONf_plane_restr0.003796
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.60010.3541300.2798237888
2.6001-2.71840.32121260.2911250790
2.7184-2.86170.31781240.2899259994
2.8617-3.04090.31081490.2864261396
3.0409-3.27560.30411350.2806269897
3.2756-3.6050.27481440.2514270498
3.605-4.12610.26831650.23270599
4.1261-5.19650.24191340.1882278299
5.1965-38.37650.20351700.2023279799

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