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- PDB-5ee3: COMPLEX STRUCTURE OF OSYCHF1 WITH AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 5ee3
TitleCOMPLEX STRUCTURE OF OSYCHF1 WITH AMP-PNP
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-like / TGS domain profile. / TGS / 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-like / TGS domain profile. / TGS / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Obg-like ATPase 1
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 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 / struct_conn
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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Obg-like ATPase 1
B: Obg-like ATPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,58014
Polymers88,9722
Non-polymers1,60812
Water32418
1
A: Obg-like ATPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3617
Polymers44,4861
Non-polymers8756
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-10 kcal/mol
Surface area18110 Å2
MethodPISA
2
B: Obg-like ATPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2197
Polymers44,4861
Non-polymers7336
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-10 kcal/mol
Surface area18040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.086, 112.390, 115.023
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 44485.887 Da / Num. of mol.: 2
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

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Non-polymers , 6 types, 30 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 20852 / Num. obs: 20818 / % possible obs: 99.9 % / Redundancy: 7.6 % / Net I/σ(I): 19.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementResolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.902 / SU B: 17.477 / SU ML: 0.325 / Cross valid method: THROUGHOUT / ESU R Free: 0.41 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26076 1060 5.1 %RANDOM
Rwork0.22722 ---
obs0.22897 19709 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.011 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20 Å2-0 Å2
2---1.53 Å20 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5496 0 90 18 5604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195705
X-RAY DIFFRACTIONr_bond_other_d0.0010.025167
X-RAY DIFFRACTIONr_angle_refined_deg1.1631.9657747
X-RAY DIFFRACTIONr_angle_other_deg0.87311884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9355715
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77424.72250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8815883
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3731523
X-RAY DIFFRACTIONr_chiral_restr0.0610.2861
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216456
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021283
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_it2.1586.5322878
X-RAY DIFFRACTIONr_mcbond_other2.1586.5322877
X-RAY DIFFRACTIONr_mcangle_it3.6529.7873587
X-RAY DIFFRACTIONr_mcangle_other3.6519.7883588
X-RAY DIFFRACTIONr_scbond_it1.8826.6462827
X-RAY DIFFRACTIONr_scbond_other1.8776.642824
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1979.9134155
X-RAY DIFFRACTIONr_long_range_B_refined5.40851.5526145
X-RAY DIFFRACTIONr_long_range_B_other5.40851.5576146
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.895→2.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 64 -
Rwork0.357 1346 -
obs--92.7 %

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