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- PDB-2yv5: Crystal structure of Yjeq from Aquifex aeolicus -

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Basic information

Entry
Database: PDB / ID: 2yv5
TitleCrystal structure of Yjeq from Aquifex aeolicus
ComponentsYjeQ protein
KeywordsHYDROLASE / GTPASE / PERMUTATION / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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 / Small ribosomal subunit biogenesis GTPase RsgA
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWang, H. / Kaminishi, T. / Hanawa-Suetsugu, K. / Takemoto, C. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of YjeQ from Aquifex aeolicus
Authors: Wang, H. / Kaminishi, T. / Hanawa-Suetsugu, K. / Takemoto, C. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionApr 9, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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_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: YjeQ protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3404
Polymers34,7961
Non-polymers5443
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.139, 63.139, 157.319
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein YjeQ protein


Mass: 34796.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: YjeQ / Plasmid: pET25b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A4PIH2, UniProt: O66555*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GDP / GUANOSINE-5'-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


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.25 Å3/Da / Density % sol: 45.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: PEG 3350, Ammonium nitratre, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 25896 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 18.7 % / Biso Wilson estimate: 14.1 Å2 / Rsym value: 0.084 / Net I/σ(I): 34.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 18.7 % / Mean I/σ(I) obs: 12.5 / Num. unique all: 2532 / Rsym value: 0.249 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U0L

1u0l


Resolution: 1.9→42.95 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 540315.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1234 4.8 %RANDOM
Rwork0.176 ---
obs0.176 25585 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.1979 Å2 / ksol: 0.389417 e/Å3
Displacement parametersBiso mean: 26.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å20 Å2
2---0.98 Å20 Å2
3---1.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a--0.08 Å
Refinement stepCycle: LAST / Resolution: 1.9→42.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2367 0 30 218 2615
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d0.97
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.206 210 5.1 %
Rwork0.155 3916 -
obs--97.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramgdp_cns_top
X-RAY DIFFRACTION3gdp_cns_paramion.top
X-RAY DIFFRACTION4ion.param

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