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- PDB-5ee1: Crystal structure of OsYchF1 at pH 7.85 -

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Basic information

Entry
Database: PDB / ID: 5ee1
TitleCrystal structure of OsYchF1 at pH 7.85
ComponentsObg-like ATPase 1
KeywordsHYDROLASE / osychf1 / GTP-BINDING PROTEIN / ATP / AMP-PNP / YchF-type / P-Loop NTPase
Function / homology
Function and homology information


negative regulation of response to salt stress / negative regulation of defense response to bacterium / ribosomal large subunit binding / response to salt stress / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GTPase activity / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding ...negative regulation of response to salt stress / negative regulation of defense response to bacterium / ribosomal large subunit binding / response to salt stress / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GTPase activity / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Obg-related GTPase Ych/YyaF, coiled-coil domain / Ribosome-binding ATPase YchF/Obg-like ATPase 1 / YchF, C-terminal domain / TGS-like domain superfamily / YchF, N-terminal / Protein of unknown function (DUF933) / TGS domain profile. / TGS / TGS-like / OBG-type guanine nucleotide-binding (G) domain ...Obg-related GTPase Ych/YyaF, coiled-coil domain / Ribosome-binding ATPase YchF/Obg-like ATPase 1 / YchF, C-terminal domain / TGS-like domain superfamily / YchF, N-terminal / Protein of unknown function (DUF933) / TGS domain profile. / TGS / TGS-like / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. / Beta-grasp domain / 50S ribosome-binding GTPase / GTP binding domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / DNA polymerase; domain 1 / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.55 Å
AuthorsLi, X. / Chen, Z.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: ATP binding by the P-loop NTPase OsYchF1 (an unconventional G protein) contributes to biotic but not abiotic stress responses
Authors: Cheung, M.-Y. / Li, X. / Miao, R. / Fong, Y.-H. / Li, K.-P. / Yung, Y.-L. / Yu, M.-H. / Wong, K.-B. / Chen, Z. / Lam, H.-M.
History
DepositionOct 22, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Obg-like ATPase 1


Theoretical massNumber of molelcules
Total (without water)44,4861
Polymers44,4861
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18170 Å2
Unit cell
Length a, b, c (Å)56.037, 70.394, 117.372
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Obg-like ATPase 1 / Ribosome-binding ATPase YchF / OsYchF1


Mass: 44485.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: OS08G0199300, OSYCHF1 / Plasmid: PRSETA-HISSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q6Z1J6, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.85 / Details: PEG

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 16008 / Num. obs: 15955 / % possible obs: 99.7 % / Redundancy: 5.4 % / Net I/σ(I): 17.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MAR345dtbdata reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.55→50 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.89 / SU B: 10.54 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.531 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26285 754 4.8 %RANDOM
Rwork0.22948 ---
obs0.23116 14816 96.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.206 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.07 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2791 0 0 23 2814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192854
X-RAY DIFFRACTIONr_bond_other_d0.0010.022678
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.9523863
X-RAY DIFFRACTIONr_angle_other_deg0.91336169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3975360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04324.918122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72515472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2931510
X-RAY DIFFRACTIONr_chiral_restr0.0780.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213219
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02633
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.183.8081449
X-RAY DIFFRACTIONr_mcbond_other2.183.8061448
X-RAY DIFFRACTIONr_mcangle_it3.6345.6961806
X-RAY DIFFRACTIONr_mcangle_other3.6335.6981807
X-RAY DIFFRACTIONr_scbond_it1.9723.8691405
X-RAY DIFFRACTIONr_scbond_other1.9723.8711406
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3135.7362058
X-RAY DIFFRACTIONr_long_range_B_refined5.2329.2673092
X-RAY DIFFRACTIONr_long_range_B_other5.20929.2413089
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.526→2.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 38 -
Rwork0.297 754 -
obs--67.75 %

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