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

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Basic information

Entry
Database: PDB / ID: 9rsy
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 / ASCORBIC ACID / : / aminocyclopropanecarboxylate oxidase
Similarity search - Component
Biological speciesAmborella trichopoda (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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)36,2934
Polymers35,9601
Non-polymers3333
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.267, 58.547, 112.550
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
Details: The synthetic CDNA of AmtACCO2 was fused with His-SUMO tag at N-terminus. The Expression vector is pETite N-His SUMO from Lucigen, USA.
Source: (gene. exp.) Amborella trichopoda (plant) / Gene: AMTR_s00112p00098670 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: W1NXW4, aminocyclopropanecarboxylate oxidase
#2: 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
#3: Sugar ChemComp-ASC / ASCORBIC ACID / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O6 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 1.98 Å3/Da / Density % sol: 37.78 %
Description: gold bar shaped, size various up to 0.7 millimeter in lenght.
Crystal growTemperature: 295.15 K / Method: evaporation / pH: 9.5
Details: under anaerobic condition. 25-28% PEG 3350, 0.1 M CHES pH 9.5, 3 mM ammonium iron (II) sulphate hexahydrate. microseeding. the Crystal was soaked with 500 mM ascorbate in mother liquor for 7 hours to overnight.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.94055 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94055 Å / Relative weight: 1
ReflectionResolution: 1.42→58.55 Å / Num. obs: 54268 / % possible obs: 99 % / Redundancy: 13.6 % / Biso Wilson estimate: 14.82 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.023 / Rrim(I) all: 0.086 / Net I/σ(I): 14.6
Reflection shellResolution: 1.42→1.44 Å / Rmerge(I) obs: 1.502 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2612 / CC1/2: 0.761 / Rpim(I) all: 0.411 / Rrim(I) all: 1.558

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→56.27 Å / SU ML: 0.1729 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.1831
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1859 2076 3.83 %
Rwork0.1658 52087 -
obs0.1665 54163 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.53 Å2
Refinement stepCycle: LAST / Resolution: 1.42→56.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2468 0 20 167 2655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00872579
X-RAY DIFFRACTIONf_angle_d0.97013489
X-RAY DIFFRACTIONf_chiral_restr0.0872373
X-RAY DIFFRACTIONf_plane_restr0.0108451
X-RAY DIFFRACTIONf_dihedral_angle_d16.96651001
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.450.34851530.34433348X-RAY DIFFRACTION97.03
1.45-1.490.33541270.30523432X-RAY DIFFRACTION98.15
1.49-1.530.27551340.25273417X-RAY DIFFRACTION99.33
1.53-1.570.24041370.22043401X-RAY DIFFRACTION98.55
1.57-1.630.22991520.21433428X-RAY DIFFRACTION98.62
1.63-1.680.23641480.20463424X-RAY DIFFRACTION98.89
1.68-1.750.22491290.1843446X-RAY DIFFRACTION99.03
1.75-1.830.19891270.17173486X-RAY DIFFRACTION99.23
1.83-1.930.20391240.14953381X-RAY DIFFRACTION96.9
1.93-2.050.18661650.14923488X-RAY DIFFRACTION99.62
2.05-2.210.17891210.14783492X-RAY DIFFRACTION99.61
2.21-2.430.16051250.14013556X-RAY DIFFRACTION99.86
2.43-2.780.17921610.15123523X-RAY DIFFRACTION99.97
2.78-3.50.16761350.15143542X-RAY DIFFRACTION98.58
3.5-56.270.15541380.15833723X-RAY DIFFRACTION98.62
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)
11.44300646576-1.290916342460.01244085961343.998514424040.01577526801382.827538145160.014449663309-0.481477653926-0.2911052231980.677519196949-0.000413092698758-0.03613310533960.405627186779-0.0992483257322-0.03644066673930.284084217057-0.0371674580857-0.00137207076630.2330413461070.04698183076920.146717580679-6.43584252104-3.842319373122.07933069268
24.27908560943-0.478528089723.76646671092.5405039169-1.57316276488.497030738150.06770631254390.2740783925460.370581839486-0.2354472355210.1015435497220.273811276046-0.305691074008-0.243464323426-0.1597305095490.1886297101880.02110350001140.02702103046030.17565305530.03431924789280.238736530507-12.832806154121.13382404-16.2580696239
34.31857952682-0.6051737050220.5816834565392.81423862352-0.6221483054221.86542968643-0.04939156206310.5134058131670.0824505287205-0.1542815126440.0447053556498-0.106996404652-0.1185738115030.026493033350.02504962616370.1840448328310.003699629896410.0326086555530.2221547207780.02010747900810.129355993642-4.8571175462214.8463137034-20.6061896569
41.63091818206-1.041380561530.5878055057838.5600031728-1.704818036451.976403486710.00597048624665-0.1663948630320.05860595853580.369703938993-0.021478302016-0.385044590647-0.05857177878190.1643120610220.007255479625610.160711869401-0.0225100672762-0.01959185315560.219863814588-0.006224575921850.1382233559333.001029497538.06656605822-5.43398983152
52.305054074830.0286979308735-0.3550510275331.338789241070.4459810814481.091984300570.1002024796550.0147489345867-0.1528808337550.09263173921040.0266510736175-0.2580196578640.1474646838010.213891903791-0.05518574237910.1640056516240.00119505242541-0.0351000199680.182488947775-0.0260638536990.1530602951436.04842302851.0577555577-12.8916392738
61.87579024503-0.162285291543-0.09836968997921.057809267330.2285880039610.9722732439560.03779331144630.0593974007632-0.07684871191290.102324687825-0.05910350503080.05705609058980.0957390568641-0.08492763938950.007944376038310.147513665276-0.02075102701240.003225836503590.149519612279-0.01074633923930.118003129908-10.17697294850.954896813385-13.131433711
73.98583659363-0.581406480956-0.3151109936124.379833923490.009088217878842.600094200980.07327982449780.302656624451-0.2298625092-0.06492047370570.0213026483085-0.0525977100620.245660152024-0.0665062037781-0.1217676970320.214586781798-0.00964310222912-0.001516886137350.254009203777-0.07693960034320.172098888015-0.757518275007-8.28826526489-23.2479546041
85.9737017256-4.00688040098-1.710799836862.717810836281.338843896471.98116850586-0.1315813574080.0775889728515-0.2357413872120.06102823133050.0998962834488-0.075583569750.0909863080440.08921755037050.1011901553130.201574938324-0.00264207001909-0.003166312409840.227362097165-0.07376548706970.1896008529162.33567436741-12.3577684617-28.5656934815
91.82577923108-0.7196536946350.6600292443231.014343586471.480839723135.98936775866-0.0562469288409-0.2756547546750.012491622247-0.449222195376-0.06634359883690.63468892632-0.559821869126-0.0637475142120.1418089219430.280329602731-0.00407528377017-0.1137632752570.21995772231-0.06722898471130.310536254304-9.927122623193.96451460458-14.3621198796
103.026980217931.763783629351.260251411751.792193211671.987872581292.5802057156-0.483047570221-0.13125533361-0.323391329267-0.122118153498-0.354082875981-0.4473297588370.159069496830.225600515480.8128536714471.0891639422-0.2402268178270.1798990562310.445519467902-0.1354490435610.70710363599-3.027866395393.53565205976-19.827986373
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 76 )A44 - 7643 - 75
33chain 'A' and (resid 77 through 107 )A77 - 10776 - 103
44chain 'A' and (resid 108 through 136 )A108 - 136104 - 132
55chain 'A' and (resid 137 through 163 )A137 - 163133 - 159
66chain 'A' and (resid 164 through 267 )A164 - 267160 - 263
77chain 'A' and (resid 268 through 294 )A268 - 294264 - 290
88chain 'A' and (resid 295 through 311 )A295 - 311291 - 307
99chain 'A' and (resid 401 )B4011
1010chain 'A' and (resid 402 )C402

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