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

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Basic information

Entry
Database: PDB / ID: 9rzi
TitleCrystal structure of Amborella trichopoda ACCO2 in complex with Fe and ACC
Componentsaminocyclopropanecarboxylate oxidase
KeywordsPLANT PROTEIN / aminocyclopropanecarboxylate ethylene oxidoreductase / 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 / : / NITRIC OXIDE / aminocyclopropanecarboxylate oxidase
Similarity search - Component
Biological speciesAmborella trichopoda (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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)36,2235
Polymers35,8291
Non-polymers3944
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-15 kcal/mol
Surface area14820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.590, 58.380, 114.620
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: 35828.898 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, 216 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-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.04 Å3/Da / Density % sol: 39.57 %
Description: Gold bar shaped with various size upto 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. Microseeding was carried out. The crystal was soaked with nitric oxide ...Details: Under anaerobic condition. 25-28% PEG3350, 0.1 M CHES pH 9.5, 3 mM ammonium iron (II) sulphate hexahydrate, 30 mM ACC. Microseeding was carried out. The crystal was soaked with nitric oxide saturated well solution for 30 min., and flash frozen in liquid nitrogen.

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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: May 11, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94056 Å / Relative weight: 1
ReflectionResolution: 1.45→40.9 Å / Num. obs: 52213 / % possible obs: 99.1 % / Redundancy: 13.4 % / Biso Wilson estimate: 16.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.037 / Rrim(I) all: 0.136 / Net I/σ(I): 10.7
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 14 % / Rmerge(I) obs: 5.745 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 2548 / CC1/2: 0.305 / Rpim(I) all: 1.567 / Rrim(I) all: 5.958 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→40.9 Å / SU ML: 0.254 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.7836
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2325 2708 5.22 %
Rwork0.1989 49204 -
obs0.2006 51912 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.64 Å2
Refinement stepCycle: LAST / Resolution: 1.45→40.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2459 0 23 212 2694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672567
X-RAY DIFFRACTIONf_angle_d0.9443468
X-RAY DIFFRACTIONf_chiral_restr0.0853369
X-RAY DIFFRACTIONf_plane_restr0.01448
X-RAY DIFFRACTIONf_dihedral_angle_d14.2381987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.480.51221450.50762387X-RAY DIFFRACTION93.05
1.48-1.50.51871350.46632494X-RAY DIFFRACTION95.6
1.5-1.540.45141240.43082556X-RAY DIFFRACTION98.82
1.54-1.570.41441470.38772537X-RAY DIFFRACTION97.28
1.57-1.610.38561460.36372513X-RAY DIFFRACTION98.01
1.61-1.650.34981400.33672552X-RAY DIFFRACTION98.75
1.65-1.690.33441330.30582578X-RAY DIFFRACTION97.83
1.69-1.740.32961670.29162544X-RAY DIFFRACTION98.37
1.74-1.80.29521400.26692565X-RAY DIFFRACTION99.3
1.8-1.860.31761170.2492610X-RAY DIFFRACTION98.7
1.86-1.930.26711410.21262561X-RAY DIFFRACTION98.72
1.93-2.020.22531280.19722626X-RAY DIFFRACTION99.03
2.02-2.130.20861690.18922578X-RAY DIFFRACTION99.24
2.13-2.260.24311360.17822627X-RAY DIFFRACTION99.39
2.26-2.440.19711510.16592624X-RAY DIFFRACTION99.28
2.44-2.680.21891530.1712634X-RAY DIFFRACTION99.86
2.68-3.070.23011450.17782672X-RAY DIFFRACTION99.82
3.07-3.870.18231450.15992695X-RAY DIFFRACTION99.96
3.87-40.90.18851460.16732851X-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)
11.46631530610.6294502469670.01177428436554.676047596770.6478399277863.929299550990.04860529861450.5165986728020.190495487713-0.630716042149-0.000208438963399-0.111711941241-0.490572174246-0.0301464293477-0.02157777039340.3334456241040.04448242007940.01833867994430.3959002523730.03994901958140.177078404148-6.379061883794.05235988736-1.46909594433
25.954588329540.77429634502-2.928014194353.68251004221-1.293627222692.128505737680.118779105244-0.412515038307-0.449150075710.4048351892190.05189895016560.4225627949950.2878582075710.0750882075921-0.1107264989520.292121066432-0.00727295819312-0.007494444289120.2787104018110.02479468627150.279835672424-12.5138232394-21.832527548215.431161781
31.648686062820.91215844221-0.2814753955242.92521831166-0.5198611616481.662535539470.0591012018252-0.0244342510585-0.068487185582-0.09436791444340.030714074643-0.2000932795560.04599573732530.155142828481-0.1108383990590.17734302790.0343734391021-0.002592028760020.315807978756-0.01923177548330.153358650231.21670596668-8.5875805860913.1106145442
41.784907888690.4623345580760.08305198739541.136402030140.3101885580191.087656289230.0787470914473-0.0408811140510.0425304113985-0.0995779897429-0.07509928622350.0783359539583-0.0701082720584-0.0797728197419-0.01505841875790.194901712620.02403040341210.001532447151580.281789719639-0.009125778712110.16245032154-10.3284246496-1.1859509125313.5553396153
52.54302646170.3044087479420.1879777584576.85039374818-2.298099704794.361843779240.10935684485-0.1398262492620.1149731766720.1329906554410.07682869738940.163486560661-0.0515080258267-0.0585024408209-0.1894272596660.2491080497530.008270537976970.03162754049890.451835329359-0.08155348727760.223193703925-0.8387812935917.6097155308723.8793067504
64.293074138780.9306826351596.251761833196.570533544892.863193466099.4673570144-0.3240768195630.2037233070550.224296646842-0.2008383100490.140553216468-0.199365485997-0.5627269600440.132466717940.1663278948670.286546963626-0.0190354296020.02746906274970.322889347176-0.02021185971610.2026191629452.4614923738411.768861780629.3027620484
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 163 )76 - 16375 - 158
44chain 'A' and (resid 164 through 267 )164 - 267159 - 262
55chain 'A' and (resid 268 through 294 )268 - 294263 - 289
66chain 'A' and (resid 295 through 311 )295 - 311290 - 306

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