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- PDB-9sbe: Crystal structure of Amborella trichopoda ACCO2 mutant - Y163F in... -

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Basic information

Entry
Database: PDB / ID: 9sbe
TitleCrystal structure of Amborella trichopoda ACCO2 mutant - Y163F in complex with Fe and ACC
Componentsaminocyclopropanecarboxylate oxidase
KeywordsPLANT PROTEIN / aminocyclopropanecarboxylate ethylene oxidase plant hormone
Function / homology1-AMINOCYCLOPROPANECARBOXYLIC ACID / :
Function and homology information
Biological speciesAmborella trichopoda (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75001 Å
AuthorsSun, Y. / Dhingra, S. / Allen, M.D. / Zhang, Z. / Brewitz, L. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V003291/1 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of Amborella trichopoda ACCO2 mutant - Y163F in complex with Fe and ACC
Authors: Sun, Y. / Dhingra, S. / Allen, M.D. / Zhang, Z. / Brewitz, L. / Schofield, C.J.
History
DepositionAug 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: aminocyclopropanecarboxylate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9733
Polymers35,8131
Non-polymers1602
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-13 kcal/mol
Surface area14650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.078, 56.257, 113.766
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein aminocyclopropanecarboxylate oxidase


Mass: 35812.898 Da / Num. of mol.: 1 / Mutation: Y163F
Source method: isolated from a genetically manipulated source
Details: UniParc ID- UPI0005D2D86B / Source: (gene. exp.) Amborella trichopoda (plant) / Gene: AMTR_s00112p00098670 / Plasmid: pET28a-His-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: aminocyclopropanecarboxylate oxidase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-1AC / 1-AMINOCYCLOPROPANECARBOXYLIC ACID


Type: peptide linking / Mass: 101.104 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.92 Å3/Da / Density % sol: 36.09 % / Description: Needle-like shape
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5
Details: 0.09 M Halogens (0.3M Magnesium chloride hexahydrate; 0.3M calcium chloride dihydrate) 0.1M Buffer System 2 (1.0M Sodium HEPES/MOPS(acids); pH 7.5) 50% v/v Precipitant Mix 1 (40% v/v PEG ...Details: 0.09 M Halogens (0.3M Magnesium chloride hexahydrate; 0.3M calcium chloride dihydrate) 0.1M Buffer System 2 (1.0M Sodium HEPES/MOPS(acids); pH 7.5) 50% v/v Precipitant Mix 1 (40% v/v PEG 500* MME; 20% w/v PEG 20000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.7838 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7838 Å / Relative weight: 1
ReflectionResolution: 1.61→43.08 Å / Num. obs: 28739 / % possible obs: 99.9 % / Redundancy: 13.7 % / Biso Wilson estimate: 24.42 Å2 / CC1/2: 1 / Net I/σ(I): 16.7
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 1572 / CC1/2: 0.903

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75001→34.34 Å / SU ML: 0.168 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9265
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1955 1373 4.79 %
Rwork0.1849 27280 -
obs0.1855 28653 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.42 Å2
Refinement stepCycle: LAST / Resolution: 1.75001→34.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2451 0 8 149 2608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00692535
X-RAY DIFFRACTIONf_angle_d0.82483423
X-RAY DIFFRACTIONf_chiral_restr0.0567365
X-RAY DIFFRACTIONf_plane_restr0.0065445
X-RAY DIFFRACTIONf_dihedral_angle_d5.7282340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75001-1.810.33651250.28222717X-RAY DIFFRACTION99.82
1.81-1.890.27081290.2432664X-RAY DIFFRACTION99.79
1.89-1.970.22071260.19742703X-RAY DIFFRACTION99.96
1.97-2.070.20571480.19032674X-RAY DIFFRACTION99.89
2.07-2.20.18781360.18812681X-RAY DIFFRACTION99.89
2.2-2.370.20571270.18312714X-RAY DIFFRACTION99.89
2.38-2.610.22981290.18852718X-RAY DIFFRACTION99.93
2.61-2.990.18311470.18012732X-RAY DIFFRACTION99.93
2.99-3.770.18511500.16422774X-RAY DIFFRACTION100
3.77-34.340.17691560.18152903X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -5.33412309623 Å / Origin y: -3.1212220486 Å / Origin z: 13.423963561 Å
111213212223313233
T0.142682972377 Å20.00880548110388 Å20.00593307547167 Å2-0.246844946001 Å2-0.0186618578748 Å2--0.131994693509 Å2
L1.64150950762 °20.0632374048359 °2-0.112700274831 °2-1.31370930397 °2-0.0189926238113 °2--1.28555184555 °2
S0.020880178952 Å °-0.30140518415 Å °0.0460327879602 Å °0.0453960515913 Å °-0.00143589036783 Å °0.000356229009756 Å °-0.0466887327881 Å °0.0367248608304 Å °-0.0252427529135 Å °
Refinement TLS groupSelection details: chain A

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