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

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Basic information

Entry
Database: PDB / ID: 9rsz
TitleCrystal structure of Amborella trichopoda ACCO2 in complex with Fe and ACC
Componentsaminocyclopropanecarboxylate oxidase
KeywordsOXIDOREDUCTASE / aminocyclopropanecarboxylate ethylene oxidase plant hormone / PLANT PROTEIN
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: 1.6 Å
AuthorsZhang, Z. / 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: Structures and Mechanisms of Amborella ACC oxidase
Authors: Zhang, Z. / Schofield, C.J.
History
DepositionJul 1, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 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)36,3274
Polymers35,9601
Non-polymers3673
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-10 kcal/mol
Surface area15100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.562, 58.618, 113.181
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: 35960.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amborella trichopoda (plant) / Gene: AMTR_s00112p00098670 / 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: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.01 Å3/Da / Density % sol: 38.78 % / Description: gold bar shaped in various sizes.
Crystal growTemperature: 295.15 K / Method: evaporation / pH: 9.5 / Details: 0.1 M CHES pH9.5, 25% PEG 3350, microseeding.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 1.6→52.06 Å / Num. obs: 39112 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 21.81 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.04 / Rrim(I) all: 0.149 / Net I/σ(I): 9.7
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 2.171 / Num. unique obs: 1946 / CC1/2: 0.564 / Rpim(I) all: 0.629 / Rrim(I) all: 2.263

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→52.05 Å / SU ML: 0.1945 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.4626
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2003 1953 5.01 %
Rwork0.1741 37046 -
obs0.1754 38999 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.38 Å2
Refinement stepCycle: LAST / Resolution: 1.6→52.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2468 0 21 193 2682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00642565
X-RAY DIFFRACTIONf_angle_d0.88773466
X-RAY DIFFRACTIONf_chiral_restr0.0855370
X-RAY DIFFRACTIONf_plane_restr0.0083447
X-RAY DIFFRACTIONf_dihedral_angle_d14.4808990
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.3271210.31572603X-RAY DIFFRACTION98.84
1.64-1.680.33851390.3022584X-RAY DIFFRACTION98.48
1.68-1.730.31361440.29822589X-RAY DIFFRACTION99.89
1.73-1.790.29121290.25382623X-RAY DIFFRACTION99.96
1.79-1.850.25751260.222604X-RAY DIFFRACTION99.82
1.85-1.930.23371430.18522644X-RAY DIFFRACTION99.93
1.93-2.020.22391350.17192636X-RAY DIFFRACTION100
2.02-2.120.23231410.1842610X-RAY DIFFRACTION100
2.12-2.250.22091280.15922661X-RAY DIFFRACTION99.79
2.25-2.430.15621470.15332647X-RAY DIFFRACTION99.43
2.43-2.670.19551440.15742639X-RAY DIFFRACTION99.96
2.67-3.060.1951510.17012674X-RAY DIFFRACTION99.93
3.06-3.850.17871590.15152699X-RAY DIFFRACTION99.9
3.86-52.050.16931460.15732833X-RAY DIFFRACTION99.47
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.45084145295-0.4357891566740.3085550665973.39440560295-0.2174776073612.426452170120.112126198708-0.5361596076360.3014773450050.802474941899-0.09733069674240.237409945914-0.4757606105520.0008705084745630.01354955687530.398543281327-0.05612365236130.03293241081520.272985038778-0.04800524140870.1914840064656.371658416023.598367148341.86405537579
25.20323875228-0.362989321761-3.719157238963.286808179491.623352053333.42905765391-0.07641939934620.414803653092-0.599588255161-0.04824224915650.059183531538-0.240004109290.429820115862-0.07368258042770.04460099894840.208641786680.00532865144611-0.05562398323070.216007848367-0.03527685736910.29323519174312.5942339718-21.3878406501-15.6263807768
33.06170803658-0.725834731233-0.3288043436223.432832136510.5677296493782.35632634150.009287624715780.566300166024-0.101393065143-0.2517955312970.04564884383250.02271484507150.1275390737940.03218129052470.007448818433450.1955314801620.0106228372893-0.04114957299150.219297785005-0.02478741269260.1390646893625.57341648125-15.159106177-21.1335755236
41.96816889676-1.13168091116-0.5893668184029.585412543162.299450840192.90983469930.0179951043939-0.192688046852-0.1463102439250.545904449856-0.0738994344450.5226454097250.162491483881-0.1824080174350.05930523847780.182287803263-0.0400348804550.01895759321130.2353971440320.01628727406410.164792064211-2.85391126627-8.13307487881-5.48801458563
52.18984477308-0.2353144552210.1818982610481.56870661881-0.3637600446121.365518902540.04222440661530.02093928480570.1149942803490.129176877302-0.03668426109820.0270479756336-0.106626430113-0.000235947846285-0.01565372771710.154144662234-0.02120384816440.004341189859170.1384913501090.006577859332860.1086241570176.95481788421-1.1825557838-13.2551657148
64.09611003877-0.811718686547-0.1090254278253.87929705238-0.4308452018722.871296211060.1702729700080.3356120953870.274455976572-0.09575023183340.0173944037835-0.0563878144335-0.2644200365160.0375493968888-0.1594673987130.229771904563-0.01523197903090.005749798122560.2760470483310.06485457158190.2010985310350.8866871509737.95443077943-23.5242180933
74.01569057035-1.579522628554.8468146972.90405258588-2.16620900515.90686798691-0.384219021712-0.3608712097920.2931322153680.2320901150790.2838858926630.172754281439-0.261672711778-0.3361687515040.1589062395440.2491471922260.00767777701630.0129983557750.277344477970.05205327869710.257256100209-2.2710812919412.1516554195-28.6442697815
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 43 )2 - 431 - 42
22chain 'A' and (resid 44 through 75 )44 - 7543 - 74
33chain 'A' and (resid 76 through 107 )76 - 10775 - 103
44chain 'A' and (resid 108 through 136 )108 - 136104 - 132
55chain 'A' and (resid 137 through 267 )137 - 267133 - 263
66chain 'A' and (resid 268 through 294 )268 - 294264 - 290
77chain 'A' and (resid 295 through 311 )295 - 311291 - 307

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