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- PDB-3cno: GDP-bound structue of TM YlqF -

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Basic information

Entry
Database: PDB / ID: 3cno
TitleGDP-bound structue of TM YlqF
ComponentsPutative uncharacterized protein
KeywordsSIGNALING PROTEIN / YlqF / circular permutation / GDP
Function / homology
Function and homology information


translation / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Conserved Hypothetical Protein Ylqf; Chain: A; domain 2 - #10 / Conserved Hypothetical Protein Ylqf; Chain: A; domain 2 / GTPase, MTG1 / GTP-binding protein, ribosome biogenesis / GTP-binding protein, orthogonal bundle domain superfamily / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / 50S ribosome-binding GTPase / GTP binding domain / P-loop containing nucleotide triphosphate hydrolases ...Conserved Hypothetical Protein Ylqf; Chain: A; domain 2 - #10 / Conserved Hypothetical Protein Ylqf; Chain: A; domain 2 / GTPase, MTG1 / GTP-binding protein, ribosome biogenesis / GTP-binding protein, orthogonal bundle domain superfamily / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / 50S ribosome-binding GTPase / GTP binding domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ribosome biogenesis GTPase A
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKim, D.J. / Jang, J.Y. / Yoon, H.-J. / Suh, S.W.
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of YlqF, a circularly permuted GTPase: Implications for its GTPase activation in 50 S ribosomal subunit assembly
Authors: Kim, D.J. / Jang, J.Y. / Yoon, H.-J. / Suh, S.W.
History
DepositionMar 26, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0862
Polymers29,6431
Non-polymers4431
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.222, 76.660, 104.895
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative uncharacterized protein / YlqF


Mass: 29642.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0768 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZM6
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES (pH 7.5), 5% (v/v) isopropanol, 20% (w/v) polyethylene glycol 4000, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.23985 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 23, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23985 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 12683 / Num. obs: 12683
Reflection shellResolution: 2.3→2.38 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PUJ

1puj


Resolution: 2.3→19.07 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.105 / SU ML: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.382 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27585 1258 10 %RANDOM
Rwork0.21482 ---
obs0.22103 12639 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.998 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--0.54 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1824 0 28 105 1957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221883
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9972530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2675225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80622.68382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.1515365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6061519
X-RAY DIFFRACTIONr_chiral_restr0.0930.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021360
X-RAY DIFFRACTIONr_nbd_refined0.1990.2865
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21272
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2106
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.27
X-RAY DIFFRACTIONr_mcbond_it0.6821.51152
X-RAY DIFFRACTIONr_mcangle_it1.22921815
X-RAY DIFFRACTIONr_scbond_it1.333815
X-RAY DIFFRACTIONr_scangle_it2.2274.5715
LS refinement shellResolution: 2.304→2.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 69 -
Rwork0.296 722 -
all-791 -
obs--87.5 %

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