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- PDB-2rcn: Crystal Structure of the Ribosomal interacting GTPase YjeQ from t... -

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Basic information

Entry
Database: PDB / ID: 2rcn
TitleCrystal Structure of the Ribosomal interacting GTPase YjeQ from the Enterobacterial species Salmonella Typhimurium.
ComponentsProbable GTPase engC
KeywordsHYDROLASE / YjeQ / gtpase / circularly permuted / GTP-binding / Nucleotide-binding
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / ribosomal small subunit biogenesis / rRNA binding / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Probable gtpase engc; domain 3 / Ribosome biogenesis GTPase RsgA / RsgA GTPase domain / RsgA GTPase / EngC GTPase domain profile. / Ribonucleotide Reductase Protein R1; domain 1 / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...Probable gtpase engc; domain 3 / Ribosome biogenesis GTPase RsgA / RsgA GTPase domain / RsgA GTPase / EngC GTPase domain profile. / Ribonucleotide Reductase Protein R1; domain 1 / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / P-loop containing nucleotide triphosphate hydrolases / Nucleic acid-binding, OB-fold / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Small ribosomal subunit biogenesis GTPase RsgA
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsNichols, C.E. / Stammers, D.K.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Structure of the ribosomal interacting GTPase YjeQ from the enterobacterial species Salmonella typhimurium.
Authors: Nichols, C.E. / Johnson, C. / Lamb, H.K. / Lockyer, M. / Charles, I.G. / Hawkins, A.R. / Stammers, D.K.
History
DepositionSep 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable GTPase engC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4294
Polymers39,8961
Non-polymers5333
Water4,468248
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Probable GTPase engC
hetero molecules

A: Probable GTPase engC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8588
Polymers79,7922
Non-polymers1,0666
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.838, 92.838, 70.227
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-360-

MG

21A-843-

HOH

DetailsThe crystallographic monomer is equivalent to the biological monomer.

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Components

#1: Protein Probable GTPase engC


Mass: 39895.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: engC / Plasmid: pMUT99 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: UniProt: Q8ZKB0, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsLIGAND GDP HAS WRONG STEREOCHEMISTRY ON THE HYDROXYL GROUPS ATTACHED TO THE RIBOSE RING

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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: 2.19 Å3/Da / Density % sol: 43.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.85 M ammonium sulphate, 0.1 M MES and 10 mM cobalt(II)chloride, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 5, 2005 / Details: Osmic multilayer optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. all: 16948 / Num. obs: 16829 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 6.1 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 16.75
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.99 / Num. unique all: 1672 / % possible all: 94.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U0L and 1T9H

1u0l

1t9h


Resolution: 2.25→27.89 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2438805.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1686 10 %RANDOM
Rwork0.199 ---
obs0.199 16812 99.3 %-
all-16948 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.7796 Å2 / ksol: 0.359131 e/Å3
Displacement parametersBiso mean: 39.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å23.64 Å20 Å2
2--1.03 Å20 Å2
3----2.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.25→27.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2175 0 30 248 2453
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it4.623.5
X-RAY DIFFRACTIONc_mcangle_it6.026
X-RAY DIFFRACTIONc_scbond_it6.665
X-RAY DIFFRACTIONc_scangle_it8.669
LS refinement shellResolution: 2.25→2.33 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.315 147 9.4 %
Rwork0.262 1422 -
obs-1573 94.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramgdp.top
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4gdp.par

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