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- PDB-1sul: Crystal Structure of the apo-YsxC -

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Basic information

Entry
Database: PDB / ID: 1sul
TitleCrystal Structure of the apo-YsxC
ComponentsGTP-binding protein YsxC
KeywordsHYDROLASE / GTP / GTPase / GTP-binding
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
Probable GTP-binding protein EngB
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 Å
AuthorsRuzheinikov, S.N. / Das, K.S. / 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 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTP-binding protein YsxC
B: GTP-binding protein YsxC


Theoretical massNumber of molelcules
Total (without water)44,1212
Polymers44,1212
Non-polymers00
Water9,116506
1
A: GTP-binding protein YsxC


Theoretical massNumber of molelcules
Total (without water)22,0601
Polymers22,0601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTP-binding protein YsxC


Theoretical massNumber of molelcules
Total (without water)22,0601
Polymers22,0601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.670, 36.520, 83.253
Angle α, β, γ (deg.)90.00, 122.16, 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.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / 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: 2.12 Å3/Da / Density % sol: 42.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Sodium acetate, PEG 4000, Tris HCL, MnCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 1, 2001
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→10 Å / Num. all: 24474 / Num. obs: 24474 / Redundancy: 2.4 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 9.9
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 2.2 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5refinement
MAR345data collection
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 2→10 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.902 / SU B: 5.208 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25084 1243 5.1 %RANDOM
Rwork0.17329 ---
obs0.17717 23172 96.36 %-
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: 17.422 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å2-0.74 Å2
2--0.07 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3040 0 0 506 3546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223098
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.9614176
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.853378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.59915619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1070.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022277
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2530.31529
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2670.5418
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.376
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2660.556
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8291.51898
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.52223081
X-RAY DIFFRACTIONr_scbond_it2.54231200
X-RAY DIFFRACTIONr_scangle_it4.2424.51095
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.414 86
Rwork0.241 1593
Refinement TLS params.Method: refined / Origin x: 10.3718 Å / Origin y: -11.5948 Å / Origin z: 69.9788 Å
111213212223313233
T0.0048 Å2-0.0051 Å20.0081 Å2-0.0081 Å2-0.0026 Å2--0.0272 Å2
L0.224 °2-0.068 °20.3015 °2-0.1961 °2-0.2146 °2--0.8498 °2
S0.0085 Å °-0.0291 Å °0.0061 Å °0.0133 Å °0.0011 Å °-0.0006 Å °-0.0083 Å °-0.0389 Å °-0.0096 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1951 - 195
2X-RAY DIFFRACTION1BB1 - 1951 - 195

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