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

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Basic information

Entry
Database: PDB / ID: 7dlw
TitleCrystal structure of Arabidopsis ACS7 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: 2.19 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)204,5679
Polymers202,9144
Non-polymers1,6535
Water5,044280
1
A: 1-aminocyclopropane-1-carboxylate synthase 7
B: 1-aminocyclopropane-1-carboxylate synthase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3325
Polymers101,4572
Non-polymers8753
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8220 Å2
ΔGint-45 kcal/mol
Surface area30050 Å2
MethodPISA
2
C: 1-aminocyclopropane-1-carboxylate synthase 7
D: 1-aminocyclopropane-1-carboxylate synthase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,2354
Polymers101,4572
Non-polymers7792
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8260 Å2
ΔGint-36 kcal/mol
Surface area29670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.877, 69.353, 85.400
Angle α, β, γ (deg.)97.700, 94.970, 106.500
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 50728.441 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: C14H20N3O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 280 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 M Tris pH 8.6, 23% (w/v) PEG 3350

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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 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 71190 / % possible obs: 96.2 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.5
Reflection shellResolution: 2.2→2.26 Å / Rmerge(I) obs: 0.474 / Num. unique obs: 5851

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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: 3PIU

3piu


Resolution: 2.19→45.2 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2408 2142 3.01 %
Rwork0.193 69022 -
obs0.1945 71164 95.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.5 Å2 / Biso mean: 50.3169 Å2 / Biso min: 25.59 Å2
Refinement stepCycle: final / Resolution: 2.19→45.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13206 0 109 280 13595
Biso mean--44.67 45.99 -
Num. residues----1654
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.19-2.240.34221220.27844022414483
2.24-2.290.32661300.26174607473795
2.29-2.360.29091430.24564607475096
2.36-2.430.29261390.24384594473395
2.43-2.50.28341400.23984478461893
2.5-2.590.31461430.23924660480397
2.59-2.70.31241520.22974701485397
2.7-2.820.27491450.21984675482097
2.82-2.970.2591480.21834694484297
2.97-3.160.26441460.21934664481096
3.16-3.40.26971470.20654617476497
3.4-3.740.23771470.18774716486398
3.74-4.280.21171480.16824699484797
4.28-5.390.20491430.1564615475896
5.39-45.20.19321490.16364673482297

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