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- PDB-9rt1: Crystal structure of Amborella trichopoda ACCO2 in complex with F... -

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Basic information

Entry
Database: PDB / ID: 9rt1
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
: / : / aminocyclopropanecarboxylate oxidase
Similarity search - Component
Biological speciesAmborella trichopoda (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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)36,1453
Polymers35,9601
Non-polymers1852
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.040, 57.700, 113.500
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-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1JJF / (1~{R},2~{R})-1-azanyl-2-ethyl-cyclopropane-1-carboxylic acid / CYTIDINE-5'-DIPHOSPHATE-2-AMINOETHANOL


Mass: 129.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 1.96 Å3/Da / Density % sol: 37.23 %
Description: gold bar shaped, various size up to 0.7 millimeter.
Crystal growTemperature: 295.15 K / Method: evaporation / pH: 9.5
Details: Under anaerobic condition. 25-27% PEG3350, 0.1 M CHES pH9.5. 30 mM (1R,2R)-1-amino-2-ethylcyclopropanecarboxylic acid, 3 mM ammonium iron (II) sulphate hexahydrate. Microseeding.

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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 X 16M / Detector: PIXEL / Date: Aug 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94054 Å / Relative weight: 1
ReflectionResolution: 1.79→51.44 Å / Num. obs: 26502 / % possible obs: 96.7 % / Redundancy: 11 % / Biso Wilson estimate: 20.37 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.05 / Rrim(I) all: 0.171 / Net I/σ(I): 8.3
Reflection shellResolution: 1.79→1.82 Å / Redundancy: 9.1 % / Rmerge(I) obs: 2.943 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1137 / CC1/2: 0.168 / Rpim(I) all: 0.968 / Rrim(I) all: 3.09 / % possible all: 85.4

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→51.44 Å / SU ML: 0.2969 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.8472
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2615 1268 4.84 %
Rwork0.2152 24927 -
obs0.2174 26195 95.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.4 Å2
Refinement stepCycle: LAST / Resolution: 1.79→51.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2445 0 10 125 2580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722516
X-RAY DIFFRACTIONf_angle_d0.7413395
X-RAY DIFFRACTIONf_chiral_restr0.0486362
X-RAY DIFFRACTIONf_plane_restr0.01440
X-RAY DIFFRACTIONf_dihedral_angle_d14.9724959
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.860.49481090.38122305X-RAY DIFFRACTION80.55
1.86-1.950.34131330.33212487X-RAY DIFFRACTION87.74
1.95-2.050.35981370.28152730X-RAY DIFFRACTION95.44
2.05-2.180.29811360.2572816X-RAY DIFFRACTION98.56
2.18-2.350.29221450.22082848X-RAY DIFFRACTION99.87
2.35-2.580.26371510.21232893X-RAY DIFFRACTION99.84
2.58-2.950.32041520.21632880X-RAY DIFFRACTION99.74
2.96-3.720.21671470.19152883X-RAY DIFFRACTION98.19
3.72-51.440.2161580.18483085X-RAY DIFFRACTION99.97
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)
12.1403761890.829731116544-0.2103715855775.182054866241.481188373623.796589642110.1709162064380.8053678001090.567834683276-0.634036154148-0.0212833490782-0.311458154504-0.532342191878-0.134741612122-0.1315311619940.2577786109460.02867959201180.02515645588230.3817464114630.09675577825210.237608996173-6.4843855174.000583943-1.5158072173
25.745422937760.718079244131-5.132155173042.70600138121-0.7163560789218.174800934220.00450558272753-0.357018245303-0.8442518623690.2413992233660.05895078184330.4484814220550.7397170978990.05238046271830.1909152186210.258812744290.0256721159593-0.007232296800850.3206886407890.1073754548290.453027623296-12.1785124766-21.301118343614.8330545242
31.605001704361.73542570644-0.506238565894.32289135041-0.9018458848212.428261178640.164246844375-0.807166240221-0.3652173950020.221240397807-0.02474303781910.0681090696562-0.03031432251090.0437771830833-0.03388986042170.2082126483620.00598479824928-0.02697413159690.409262636730.06479238076550.192156246696-5.02621659294-15.691375875620.8066357447
41.901590419350.86049350001-0.1181047004244.00072483089-0.8378667297181.15584984684-0.007170866254990.198191079215-0.154859656044-0.5525004087710.00128682630105-0.481858699710.1730724215040.19369583158-0.009471107713660.178870093180.0278286493040.03099083897510.434385903712-0.03073244874970.2371659428042.87555732505-7.969118898155.65671609442
52.144932742950.3796264546180.3135861474441.517732866430.03417244601950.9245595371060.0123232669411-0.0414850263374-0.002386643231640.01141920033710.0344562038984-0.0625151817729-0.036797388931-0.0487267044799-0.03265072534050.1830524753230.0281707162615-0.002305564554120.350696736651-0.02479883156710.174821922285-4.19087050604-3.397953209216.2443888444
62.059162452760.6836236340460.1102615990161.655773540250.4869829773131.023491383730.147878179486-0.0142480524110.165121721743-0.0697082346821-0.1545217438710.127547599032-0.0051553000088-0.120269369214-0.01334783458280.1638020922780.01938355265950.00406309311730.3163349046410.003875835647770.197503172645-8.478267790880.08502118936811.8774131379
72.04170388539-1.30122943452.951620154927.41677126502-0.4399451176195.153268538970.131612160761-0.3098711787520.02226554993160.2159517499-0.05009025615620.2996788966190.1355758556080.1279968283470.01629357337650.19111042601-0.01877266275810.05149644816290.417284774094-0.06478417944040.2450920617210.06168632880279.1551947627525.7498346441
85.280079657641.465122280742.281512321377.91246474978-6.18320334952.00005581612-0.2606914891040.0453925746873-0.0883749248277-0.1981912668370.0956076889717-0.08357581835520.3391252567520.1143830078860.2320253093190.4397146576710.2083912569710.2653647026650.6117944263430.3464593026170.489384469305-9.60743924266-4.2549684997615.1548656696
Refinement TLS group

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

IDRefine TLS-IDSelection detailsLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 43 )A2 - 431 - 42
22chain 'A' and (resid 44 through 74 )A44 - 7443 - 73
33chain 'A' and (resid 75 through 107 )A75 - 10774 - 101
44chain 'A' and (resid 108 through 136 )A108 - 136102 - 130
55chain 'A' and (resid 137 through 183 )A137 - 183131 - 177
66chain 'A' and (resid 184 through 267 )A184 - 267178 - 261
77chain 'A' and (resid 268 through 310 )A268 - 310262 - 304
88chain 'A' and (resid 402 )C402

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