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- PDB-7dly: Crystal structure of Arabidopsis ACS7 mutant in complex with PPG -

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Basic information

Entry
Database: PDB / ID: 7dly
TitleCrystal structure of Arabidopsis ACS7 mutant in complex with PPG
Components1-aminocyclopropane-1-carboxylate synthase 7
KeywordsLYASE / ACC Synthetase / Ethylene / PLANT PROTEIN
Function / homology
Function and homology information


1-aminocyclopropane-1-carboxylate synthase / 1-aminocyclopropane-1-carboxylate synthase activity / fruit ripening / ethylene biosynthetic process / pyridoxal phosphate binding / identical protein binding
Similarity search - Function
: / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-PPG / 1-aminocyclopropane-1-carboxylate synthase 7
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsHao, B. / Zhang, Y. / Li, X. / Rao, Z.
CitationJournal: Sci Adv / Year: 2021
Title: Dual activities of ACC synthase: Novel clues regarding the molecular evolution of ACS genes.
Authors: Xu, C. / Hao, B. / Sun, G. / Mei, Y. / Sun, L. / Sun, Y. / Wang, Y. / Zhang, Y. / Zhang, W. / Zhang, M. / Zhang, Y. / Wang, D. / Rao, Z. / Li, X. / Shen, Q.J. / Wang, N.N.
History
DepositionNov 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1-aminocyclopropane-1-carboxylate synthase 7
B: 1-aminocyclopropane-1-carboxylate synthase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,0174
Polymers101,2392
Non-polymers7792
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-18 kcal/mol
Surface area30980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.425, 164.425, 97.881
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein 1-aminocyclopropane-1-carboxylate synthase 7 / ACC synthase 7 / S-adenosyl-L-methionine methylthioadenosine-lyase 7


Mass: 50619.258 Da / Num. of mol.: 2 / Mutation: F97Y,Q98G,D99N,Y199F,H101R,L103G,K104E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ACS7, At4g26200, T25K17.10 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9STR4, 1-aminocyclopropane-1-carboxylate synthase
#2: Chemical ChemComp-PPG / (2E,3E)-4-(2-aminoethoxy)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]but-3-enoic acid


Mass: 389.298 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N3O8P / Feature type: SUBJECT OF INVESTIGATION
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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.6 / Details: 0.1 M HEPES pH 7.6, 6% (w/v) PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.94→50 Å / Num. obs: 20168 / % possible obs: 96.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 11.2
Reflection shellResolution: 2.95→3.06 Å / Num. unique obs: 2093 / CC1/2: 0.693

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DLW

7dlw


Resolution: 2.94→47.16 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 37.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2774 1945 9.72 %
Rwork0.2242 18063 -
obs0.2292 20008 95.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 204.8 Å2 / Biso mean: 104.8108 Å2 / Biso min: 59.94 Å2
Refinement stepCycle: final / Resolution: 2.94→47.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6376 0 52 0 6428
Biso mean--103.23 --
Num. residues----801
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.94-3.010.36681450.305413271472100
3.01-3.10.3381390.291913591498100
3.1-3.190.36381460.2941329147599
3.19-3.290.42121570.342713651522100
3.29-3.410.45321270.42961256138394
3.41-3.540.54171220.49181206132889
3.54-3.70.55121340.49791137127183
3.71-3.90.46241160.41451172128889
3.9-4.140.25381430.24441208135191
4.15-4.460.22011550.16381347150299
4.47-4.910.21781480.15311321146999
4.91-5.620.22991370.161413591496100
5.62-7.080.23561450.18381331147698
7.08-47.160.19921310.15511346147799

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