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

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Basic information

Entry
Database: PDB / ID: 9rzh
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 / BICARBONATE ION / : / aminocyclopropanecarboxylate oxidase
Similarity search - Component
Biological speciesAmborella trichopoda (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 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 15, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 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)36,3405
Polymers35,9151
Non-polymers4254
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-12 kcal/mol
Surface area14730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.587, 58.292, 114.809
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

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Protein , 1 types, 1 molecules A

#1: Protein aminocyclopropanecarboxylate oxidase


Mass: 35914.902 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

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Non-polymers , 5 types, 241 molecules

#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-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: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.03 Å3/Da / Density % sol: 39.42 %
Description: Gold bar shaped crystals with various size up to 0.5 millimeter in length.
Crystal growTemperature: 295.15 K / Method: evaporation / pH: 9.5
Details: Under anaerobic condition. 25-28% PEG3350, 0.1 M CHES pH 9.5, 3 mM ammonium iron (II) sulphate hexahydrate, 30 mM ACC. Micro-seeding was carried out. The crystal was soaked with 500 mM ...Details: Under anaerobic condition. 25-28% PEG3350, 0.1 M CHES pH 9.5, 3 mM ammonium iron (II) sulphate hexahydrate, 30 mM ACC. Micro-seeding was carried out. The crystal was soaked with 500 mM sodium bicarbonate in the well solution for 5 hours.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.94056 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94056 Å / Relative weight: 1
ReflectionResolution: 1.38→58.29 Å / Num. obs: 59878 / % possible obs: 98.1 % / Redundancy: 13.6 % / Biso Wilson estimate: 14.24 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.033 / Rrim(I) all: 0.1222 / Net I/σ(I): 8.8
Reflection shellResolution: 1.38→1.4 Å / Redundancy: 12 % / Rmerge(I) obs: 4.107 / Mean I/σ(I) obs: 0.2 / Num. unique obs: 2801 / CC1/2: 0.314 / Rpim(I) all: 1.21 / Rrim(I) all: 4.289 / % possible all: 92.9

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.38→34.91 Å / SU ML: 0.3111 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.1996
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2328 1922 3.32 %
Rwork0.2054 56054 -
obs0.2063 57976 95.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.31 Å2
Refinement stepCycle: LAST / Resolution: 1.38→34.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2448 0 25 237 2710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00522543
X-RAY DIFFRACTIONf_angle_d0.77513436
X-RAY DIFFRACTIONf_chiral_restr0.0758366
X-RAY DIFFRACTIONf_plane_restr0.0082446
X-RAY DIFFRACTIONf_dihedral_angle_d14.2535972
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.410.61670.6062295X-RAY DIFFRACTION54.85
1.41-1.450.56111600.55043975X-RAY DIFFRACTION96.3
1.45-1.50.4721520.5024049X-RAY DIFFRACTION97.63
1.5-1.540.38441420.42664048X-RAY DIFFRACTION97.94
1.54-1.60.38161270.37034086X-RAY DIFFRACTION98
1.6-1.660.35641350.32244111X-RAY DIFFRACTION98.45
1.66-1.740.31041560.28724102X-RAY DIFFRACTION98.25
1.74-1.830.32381260.24934143X-RAY DIFFRACTION98.71
1.83-1.950.23631460.1994008X-RAY DIFFRACTION95.52
1.95-2.10.20341250.17684178X-RAY DIFFRACTION99.01
2.1-2.310.20741640.1724180X-RAY DIFFRACTION99.47
2.31-2.640.19421270.16954249X-RAY DIFFRACTION99.75
2.64-3.330.22691500.17164282X-RAY DIFFRACTION99.66
3.33-34.910.16411450.15424348X-RAY DIFFRACTION96.89
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)
10.7714474778120.2780195679390.09257253303952.630525737350.3127960547682.165466203290.03534965175830.5159610992080.172604089864-0.782589209162-0.018683153362-0.110125966702-0.7362152814830.0505229814039-0.01536516301180.4818199763380.00797442395550.009821764518940.473680468070.02057206549680.204843884294-5.916306768734.17342485878-1.3371929981
23.173745074380.433764879384-0.3566437917523.88550608049-0.3658371761942.58090227308-0.0172778633994-0.200626093785-0.388949425930.3495407046260.08484128752830.2930903253020.341114698963-0.343138685406-0.03578277646720.1914648938090.001171049510410.01161530189420.430697457455-0.0008582130751150.261190341709-11.605663492-21.585742647414.2815026766
31.486297160750.27025476257-0.3205301325842.116445270630.4876039788071.527089741820.0235758800645-0.0290698516336-0.0152159968306-0.1601014526260.135116534234-0.210283724945-0.1116845485240.204214524561-0.1500633298260.1475505908330.005589425353670.0124674371690.361921631283-0.0320399810770.1557378522551.52480517201-8.557877916312.9879832079
41.733961182730.2688764193420.1347713527971.196463415480.681233994761.355184390970.0213672357121-0.08440812269910.086044146682-0.125565628993-0.008148129228850.0134786906191-0.149837807583-0.0841599379597-0.02340678410260.1552535158660.04015463887080.001161440780640.297776205865-0.01736667388890.139809703249-8.025274204870.73568298136316.0539029055
55.964052570440.7933330379942.87306636712.845869303451.539514607633.68569579934-0.2055856324710.1368567814740.0680463689212-0.1784259135220.141189378113-0.107091778071-0.1676378053020.142101299116-0.07504172497110.2473207594880.01389018081780.02841726232340.363193703156-0.03067429001410.1978646648022.3387001055911.592063767829.5174680759
61.999967324082.000023264941.999973770192.000000902742.000016208621.99998953129-0.123850612584-0.1036990349050.253986933474-0.0796333204613-0.1083126522870.302441367952-0.1618405133080.06968107483660.2756524892040.269746421098-0.08289685988060.0750331030610.105492495162-0.1126810044390.181547170444-10.0023877262-4.0919919781914.6103745509
77.315783872-7.89496234917-1.999381032188.891607148113.198341264763.71357629665-0.476924524299-0.502886338655-0.9585271836451.052068051760.8814639428711.502325072990.009643834548070.174145174858-0.3298384396960.6947630142880.125545807613-0.06938711459270.733286611336-0.06911356025980.671015167165-2.9518097916-7.7204662412924.0202915524
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 73 )A44 - 7343 - 72
33chain 'A' and (resid 74 through 163 )A74 - 16373 - 156
44chain 'A' and (resid 164 through 294 )A164 - 294157 - 287
55chain 'A' and (resid 295 through 311 )A295 - 311288 - 304
66chain 'A' and (resid 403 )C403306
77chain 'A' and (resid 404 )D404

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