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- PDB-2hjg: The crystal structure of the B. subtilis YphC GTPase in complex w... -

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Basic information

Entry
Database: PDB / ID: 2hjg
TitleThe crystal structure of the B. subtilis YphC GTPase in complex with GDP
ComponentsGTP-binding protein engA
KeywordsHYDROLASE / GTPase EngA KH-domain
Function / homology
Function and homology information


ribosome biogenesis / ribosome binding / GTP binding
Similarity search - Function
EngA-type guanine nucleotide-binding (G) domain / EngA-type guanine nucleotide-binding (G) domain profile. / GTP-binding protein EngA / GTPase Der, C-terminal KH-domain-like / KH-domain-like of EngA bacterial GTPase enzymes, C-terminal / K homology (KH) domain / 50S ribosome-binding GTPase / GTP binding domain / GMP Synthetase; Chain A, domain 3 / K homology domain-like, alpha/beta ...EngA-type guanine nucleotide-binding (G) domain / EngA-type guanine nucleotide-binding (G) domain profile. / GTP-binding protein EngA / GTPase Der, C-terminal KH-domain-like / KH-domain-like of EngA bacterial GTPase enzymes, C-terminal / K homology (KH) domain / 50S ribosome-binding GTPase / GTP binding domain / GMP Synthetase; Chain A, domain 3 / K homology domain-like, alpha/beta / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GTPase Der
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsMuench, S.P. / Xu, L. / Sedelnikova, S.E. / Rice, D.W.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: The essential GTPase YphC displays a major domain rearrangement associated with nucleotide binding.
Authors: Muench, S.P. / Xu, L. / Sedelnikova, S.E. / Rice, D.W.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Cloning, purification and preliminary crystallographic analysis of the Bacillus subtilis GTPase YphC-GDP complex.
Authors: Xu, L. / Muench, S.P. / Roujeinikova, A. / Sedelnikova, S.E. / Rice, D.W.
History
DepositionJun 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTP-binding protein engA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3434
Polymers49,3911
Non-polymers9523
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.711, 65.045, 110.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer

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Components

#1: Protein GTP-binding protein engA


Mass: 49391.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: engA / Plasmid: pMAT1 / Production host: Escherichia coli (E. coli) / Strain (production host): E. coli Tuner (DE3) / References: UniProt: P50743
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M sodium flouride, 20% (w/v) PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.9794, 0.9797, 1.0094
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 27, 2005
RadiationMonochromator: double crystal Si(III)monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97971
31.00941
ReflectionResolution: 2.5→30 Å / Num. obs: 16253 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 17.8
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.1 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→19.96 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.895 / SU B: 22.068 / SU ML: 0.232 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.633 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27353 814 5 %RANDOM
Rwork0.21539 ---
obs0.21815 15364 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.463 Å2
Baniso -1Baniso -2Baniso -3
1--2.29 Å20 Å20 Å2
2---0.61 Å20 Å2
3---2.89 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3147 0 57 31 3235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223266
X-RAY DIFFRACTIONr_bond_other_d0.0060.022974
X-RAY DIFFRACTIONr_angle_refined_deg1.2511.9774431
X-RAY DIFFRACTIONr_angle_other_deg0.76636902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.2835395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4224.459148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.34615554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.11519
X-RAY DIFFRACTIONr_chiral_restr0.0710.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023573
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02655
X-RAY DIFFRACTIONr_nbd_refined0.2020.2670
X-RAY DIFFRACTIONr_nbd_other0.1960.22930
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21593
X-RAY DIFFRACTIONr_nbtor_other0.0830.21768
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.274
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0890.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0930.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2490.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2961.52132
X-RAY DIFFRACTIONr_mcbond_other0.0621.5809
X-RAY DIFFRACTIONr_mcangle_it0.81623221
X-RAY DIFFRACTIONr_scbond_it1.86331414
X-RAY DIFFRACTIONr_scangle_it2.6444.51210
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 67 -
Rwork0.254 1076 -
obs--100 %

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