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- PDB-9rwo: Crystal structure of Amborella trichopoda ACCO2 in complex with F... -

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Basic information

Entry
Database: PDB / ID: 9rwo
TitleCrystal structure of Amborella trichopoda ACCO2 in complex with Fe and ACC
Componentsaminocyclopropanecarboxylate oxidase
KeywordsPLANT PROTEIN / aminocyclopropanecarboxylate ethylene oxidase plant hormone
Function / homology
Function and homology information


aminocyclopropanecarboxylate oxidase / 1-aminocyclopropane-1-carboxylate oxidase activity / ethylene biosynthetic process / 2-oxoglutarate-dependent dioxygenase activity / L-ascorbic acid binding / metal ion binding
Similarity search - Function
: / Non-haem dioxygenase N-terminal domain / non-haem dioxygenase in morphine synthesis N-terminal / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile.
Similarity search - Domain/homology
1-AMINOCYCLOPROPANECARBOXYLIC ACID / : / aminocyclopropanecarboxylate oxidase
Similarity search - Component
Biological speciesAmborella trichopoda (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsZhang, Z. / Schofield, C.J. / Sun, Y. / Allen, M.D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V003291/1 United Kingdom
CitationJournal: To Be Published
Title: Structures and Mechanisms of Amborella ACC oxidase
Authors: Zhang, Z. / Schofield, C.J.
History
DepositionJul 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: aminocyclopropanecarboxylate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9893
Polymers35,8291
Non-polymers1602
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-12 kcal/mol
Surface area15000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.278, 58.777, 112.724
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: 35828.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amborella trichopoda (plant) / Gene: AMTR_s00112p00098670 / Plasmid: pET28a-His-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: W1NXW4, 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.: 220 / 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: 2 Å3/Da / Density % sol: 38.52 % / Description: Needle-like crystals
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5
Details: 20 mM Xylitol, 20 mM Myo-Inositol, 20 mM D-(-)Fructose, 20 mM L-Rhamnose monohydrate, 20 uM D-Sorbitol; 100 mM BES, Triethanolamine (TEA), pH 7.5; 31% w/v Percipitant Mix 8 (10% w/v PEG ...Details: 20 mM Xylitol, 20 mM Myo-Inositol, 20 mM D-(-)Fructose, 20 mM L-Rhamnose monohydrate, 20 uM D-Sorbitol; 100 mM BES, Triethanolamine (TEA), pH 7.5; 31% w/v Percipitant Mix 8 (10% w/v PEG 20000, 50% w/v Trimethylpropane, 2% w/v NDSB 195)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.94054 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94054 Å / Relative weight: 1
ReflectionResolution: 1.65→52.1 Å / Num. obs: 35463 / % possible obs: 100 % / Redundancy: 10.7 % / Biso Wilson estimate: 21.04 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.031 / Rrim(I) all: 0.105 / Χ2: 0.85 / Net I/σ(I): 11
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 10.7 % / Rmerge(I) obs: 1.092 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1740 / CC1/2: 0.805 / Rpim(I) all: 0.343 / Rrim(I) all: 1.146 / Χ2: 0.71 / % possible all: 100

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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: 1.65→40.68 Å / SU ML: 0.2069 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8192
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2037 1760 4.98 %
Rwork0.1762 33613 -
obs0.1776 35373 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.76 Å2
Refinement stepCycle: LAST / Resolution: 1.65→40.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2480 0 8 220 2708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01142588
X-RAY DIFFRACTIONf_angle_d1.10873501
X-RAY DIFFRACTIONf_chiral_restr0.0758372
X-RAY DIFFRACTIONf_plane_restr0.01459
X-RAY DIFFRACTIONf_dihedral_angle_d7.908352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.34421320.31552528X-RAY DIFFRACTION99.03
1.69-1.740.32141250.26182554X-RAY DIFFRACTION99.81
1.74-1.80.27711460.22752519X-RAY DIFFRACTION99.81
1.8-1.860.24461210.20692566X-RAY DIFFRACTION99.96
1.86-1.940.19441250.18522546X-RAY DIFFRACTION99.37
1.94-2.030.20421430.17162561X-RAY DIFFRACTION99.89
2.03-2.130.2361430.1822563X-RAY DIFFRACTION99.93
2.13-2.270.21431370.16792571X-RAY DIFFRACTION99.89
2.27-2.440.1991310.17462584X-RAY DIFFRACTION100
2.44-2.690.22831410.16982592X-RAY DIFFRACTION99.85
2.69-3.080.1751210.1762623X-RAY DIFFRACTION100
3.08-3.880.17061340.15482649X-RAY DIFFRACTION100
3.88-40.680.19031610.16542757X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: -5.55962801771 Å / Origin y: -3.544816922 Å / Origin z: 13.403032338 Å
111213212223313233
T0.112016223181 Å20.0138101388764 Å20.00443321760676 Å2-0.159813634046 Å2-0.00287800901316 Å2--0.101646390175 Å2
L1.28949329768 °20.0707059271422 °20.0272601944774 °2-1.15623615648 °20.104149312408 °2--0.996656799939 °2
S0.0295712980929 Å °-0.0216559644608 Å °0.0445255078801 Å °-0.0203457843581 Å °-0.00926697616643 Å °0.0121318642376 Å °-0.0233398811136 Å °-0.00668720703452 Å °-0.0258251975263 Å °
Refinement TLS groupSelection details: chain A

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