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- PDB-7dk8: Crystal structure of OsGH3-8 with AMP -

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Basic information

Entry
Database: PDB / ID: 7dk8
TitleCrystal structure of OsGH3-8 with AMP
ComponentsProbable indole-3-acetic acid-amido synthetase GH3.8
KeywordsPLANT PROTEIN / acyl acid amido synthetases / auxin / active site
Function / homology
Function and homology information


intracellular auxin homeostasis / indole-3-acetic acid amido synthetase activity / auxin biosynthetic process / regulation of defense response to bacterium / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / pollen development / AMP binding / defense response
Similarity search - Function
GH3 family / GH3 auxin-responsive promoter
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Indole-3-acetic acid-amido synthetase GH3.8
Similarity search - Component
Biological speciesOryza sativa subsp. indica (long-grained rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsZhang, Y.K. / Xu, G.L. / Ming, Z.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31700052 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Crystal structure of the acyl acid amido synthetase GH3-8 from Oryza sativa.
Authors: Xu, G. / Zhang, Y. / Li, M. / Jiao, X. / Zhou, L. / Ming, Z.
History
DepositionNov 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable indole-3-acetic acid-amido synthetase GH3.8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6002
Polymers66,2531
Non-polymers3471
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-3 kcal/mol
Surface area22670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.050, 121.050, 62.670
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Probable indole-3-acetic acid-amido synthetase GH3.8 / Auxin-responsive GH3-like protein 8 / OsGH3-8


Mass: 66252.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. indica (long-grained rice)
Gene: GH3.8, OsI_025789
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A3BLS0, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 Å3/Da / Density % sol: 38.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.08M Tris pH 8.0, 0.1M Tris-HCl (pH 8.5), 22.4% (w/v) PEG 4000, 0.02M Bis-Tris pH 6.5, 5% (w/v) PEG 3350, 0.2 Microliter 275.0mM 2,6-Dimethyl-4-heptyl-beta-D-maltopyranoside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 13, 2020
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.99→30.5203 Å / Num. obs: 35491 / % possible obs: 98.44 % / Redundancy: 19.8 % / Rmerge(I) obs: 0.02218 / Net I/σ(I): 20.3
Reflection shellResolution: 1.99→2.04 Å / Rmerge(I) obs: 0.3072 / Num. unique obs: 36047

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4b2g

4b2g


Resolution: 1.99→24.578 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2556 1955 5.51 %
Rwork0.1968 33536 -
obs0.2 35491 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.62 Å2 / Biso mean: 47.5662 Å2 / Biso min: 26 Å2
Refinement stepCycle: final / Resolution: 1.99→24.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4375 0 35 183 4593
Biso mean--42.56 46.53 -
Num. residues----558
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9902-2.03990.33671380.2703229796
2.0399-2.0950.32671380.2543234496
2.095-2.15670.30121350.2419234397
2.1567-2.22620.34511320.2422234197
2.2262-2.30570.26821390.2233238798
2.3057-2.3980.31671350.223236898
2.398-2.5070.28531340.2302238799
2.507-2.6390.30551420.2266238599
2.639-2.80420.28311350.2241241999
2.8042-3.02030.28231450.22962445100
3.0203-3.32360.24991410.21442424100
3.3236-3.8030.24351470.18682432100
3.803-4.78560.24291510.16222455100
4.7856-24.570.21251430.17462509100

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