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- PDB-1svi: Crystal Structure of the GTP-binding protein YsxC complexed with GDP -

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Basic information

Entry
Database: PDB / ID: 1svi
TitleCrystal Structure of the GTP-binding protein YsxC complexed with GDP
ComponentsGTP-binding protein YSXC
KeywordsHYDROLASE / YsxC / ENGB / GTPase / GTP-binding protein / GDP
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Probable GTP-binding protein EngB
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.95 Å
AuthorsRuzheinikov, S.N. / Das, S.K. / Sedelnikova, S.E. / Baker, P.J. / Artymiuk, P.J. / Garcia-Lara, J. / Foster, S.J. / Rice, D.W.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Analysis of the Open and Closed Conformations of the GTP-binding Protein YsxC from Bacillus subtilis.
Authors: Ruzheinikov, S.N. / Das, S.K. / Sedelnikova, S.E. / Baker, P.J. / Artymiuk, P.J. / Garcia-Lara, J. / Foster, S.J. / Rice, D.W.
#1: Journal: To be Published
Title: Expression, purification, crystallization and preliminary crystallographic analysis of a putative GTP-binding protein, YsxC, from Bacillus subtilis .
Authors: Das, S.K. / Sedelnikova, S.E. / Baker, P.J. / Ruzheinikov, S.N. / Foster, S.J. / Rice, D.W.
History
DepositionMar 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: GTP-binding protein YSXC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5042
Polymers22,0601
Non-polymers4431
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.179, 68.305, 61.999
Angle α, β, γ (deg.)90.00, 94.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein GTP-binding protein YSXC


Mass: 22060.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: YsxC, ENGB, BSU28190 / Production host: Escherichia coli (E. coli) / References: UniProt: P38424
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.21 Å3/Da / Density % sol: 44.34 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PG 4000, isopropanol, N Hepes buffer, GDP,MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→10 Å / Num. obs: 13194 / % possible obs: 94.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
REFMAC5refinement
MAR345data collection
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 1.95→10 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.265 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22174 641 4.9 %RANDOM
Rwork0.17614 ---
obs0.17831 12485 94.13 %-
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: 17.442 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å2-0.58 Å2
2---0.53 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.95→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1457 0 28 246 1731
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221515
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.9822049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3973180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.49415291
X-RAY DIFFRACTIONr_chiral_restr0.0890.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021104
X-RAY DIFFRACTIONr_nbd_refined0.2350.3774
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.5197
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.343
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.630.522
X-RAY DIFFRACTIONr_mcbond_it0.5471.5906
X-RAY DIFFRACTIONr_mcangle_it1.06121471
X-RAY DIFFRACTIONr_scbond_it1.7913609
X-RAY DIFFRACTIONr_scangle_it3.0314.5578
LS refinement shellResolution: 1.95→1.999 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.309 43
Rwork0.237 887
Refinement TLS params.Method: refined / Origin x: 10.415 Å / Origin y: 34.7705 Å / Origin z: 44.6358 Å
111213212223313233
T0.0227 Å20.03 Å2-0.0041 Å2-0.0406 Å20.0004 Å2--0.0437 Å2
L1.3004 °2-0.0941 °2-0.1497 °2-1.3124 °2-0.3525 °2--2.7536 °2
S-0.0025 Å °-0.0566 Å °0.0547 Å °0.149 Å °0.0837 Å °-0.0353 Å °-0.0936 Å °-0.2315 Å °-0.0812 Å °

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