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

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Basic information

Entry
Database: PDB / ID: 9rzj
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 / BICARBONATE ION / : / NITRIC OXIDE / aminocyclopropanecarboxylate oxidase
Similarity search - Component
Biological speciesAmborella trichopoda (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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)37,05115
Polymers36,0461
Non-polymers1,00414
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-10 kcal/mol
Surface area14790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.520, 59.010, 113.600
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: 36046.094 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

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Non-polymers , 6 types, 152 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.: 10 / Source method: obtained synthetically / Formula: CHO3
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.02 Å3/Da / Density % sol: 39.21 %
Description: Gold bar shaped with size various 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, 3.0 mM ammonium iron (II) sulphate hexahydrate, 30 mM ACC. Micro-seeding was carried out. The crystals were soaked in 400 mM ...Details: Under anaerobic condition. 25-28% PEG3350, 0.1 M CHES pH 9.5, 3.0 mM ammonium iron (II) sulphate hexahydrate, 30 mM ACC. Micro-seeding was carried out. The crystals were soaked in 400 mM sodium bicarbonate in nitric oxide saturated well solution for ~30 min. to 1 hour. The crystals were 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: 1.75→40.64 Å / Num. obs: 30331 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 21.95 Å2 / CC1/2: 0.999 / R split: 0.065 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.048 / Rrim(I) all: 0.174 / Χ2: 0.99 / Net I/σ(I): 11.8
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 13.1 % / Rmerge(I) obs: 4.867 / Num. unique obs: 1474 / CC1/2: 0.347 / Rpim(I) all: 1.386 / Rrim(I) all: 5.063 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→40.64 Å / SU ML: 0.2713 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.0753
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2238 1592 5.27 %
Rwork0.1924 28644 -
obs0.1941 30236 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.4 Å2
Refinement stepCycle: LAST / Resolution: 1.75→40.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2465 0 63 138 2666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062587
X-RAY DIFFRACTIONf_angle_d0.79763483
X-RAY DIFFRACTIONf_chiral_restr0.0608368
X-RAY DIFFRACTIONf_plane_restr0.0091457
X-RAY DIFFRACTIONf_dihedral_angle_d14.5674980
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.810.37611270.3842547X-RAY DIFFRACTION99.18
1.81-1.870.39521580.34132518X-RAY DIFFRACTION99.7
1.87-1.950.30921400.27872563X-RAY DIFFRACTION99.96
1.95-2.030.25761360.23972605X-RAY DIFFRACTION99.96
2.03-2.140.29821550.23132556X-RAY DIFFRACTION99.93
2.14-2.280.24891360.20822609X-RAY DIFFRACTION99.89
2.28-2.450.23031270.18922602X-RAY DIFFRACTION100
2.45-2.70.23981350.18582614X-RAY DIFFRACTION99.96
2.7-3.090.2241720.19112598X-RAY DIFFRACTION99.96
3.09-3.890.18111630.16722634X-RAY DIFFRACTION99.96
3.89-40.640.19441430.16212798X-RAY DIFFRACTION100
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)
11.805062490371.524782684280.154651543325.227288433640.5343654093463.723641401420.07703237259720.6771533527780.397982560583-0.651679677628-0.0505709150581-0.27135988203-0.452966848836-0.232075060597-0.0792864868390.3574210334180.05801352207010.03947254014920.3594915778910.0858008929660.223164537975-6.176098709573.93095639266-1.76286707376
26.888458349220.793407942121-5.213281321963.5393856431-1.282721767026.93645171854-0.0310229203246-0.35036536403-0.5346458708990.2939914232750.1451451288570.2892295115430.5669359580190.124135830387-0.0008616371721990.264120723543-0.0110948503964-0.04463756192640.2113899917740.0294352708880.325785858543-12.5206445747-21.468894346915.5025397637
32.677377715410.943562751265-0.4581996122264.38295017372-1.461358690471.747215263340.07224867110340.017764048072-0.257778481239-0.123696129693-0.0935203984585-0.267362872510.1045116273310.04115953265010.003744380014430.2173652812760.0173316088289-0.03880325911380.284483608459-0.04495146633410.182234040438-0.755881622796-11.71310486412.9507971722
42.809582553750.286399939478-0.08462062435371.08718193570.4413800824161.208146198380.103504586988-0.03331788034110.0842525643791-0.107036824623-0.0517014246603-0.0445221104882-0.103384436118-0.0203810349684-0.05184173712030.21897887530.02488223018740.007063638880610.1947874285770.002071824906530.156041309689-6.8813896977-1.1149106332813.3224238525
53.976317213590.2136753455780.4388610419926.06811967776-1.559215959274.046577700920.289469362055-0.2789163459440.1291591637930.2118699546710.03145342500150.151737014591-0.185482915836-0.0932662838566-0.3354460547220.2570427148840.02043499837850.03796222537070.358996852769-0.0886682633450.2378228862-0.8058592041547.9455001800223.6139029395
64.132302255461.833463197355.422601107733.969510936322.676731945137.16454527539-0.4007093777740.1058748672250.452623201362-0.212600617442-0.07915977266230.00166622940569-0.400509576379-0.07782991280530.3384132425850.2860957970710.004301860580920.0174629812810.252522060406-0.04342664011340.3108505924192.4409800545612.307632645928.8467123238
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 136 )76 - 13675 - 131
44chain 'A' and (resid 137 through 267 )137 - 267132 - 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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