[English] 日本語
Yorodumi
- PDB-9rt0: Crystal structure of Amborella trichopoda ACCO2 in complex with F... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9rt0
TitleCrystal structure of Amborella trichopoda ACCO2 in complex with Fe and ACC
Componentsaminocyclopropanecarboxylate oxidase
KeywordsOXIDOREDUCTASE / aminocyclopropanecarboxylate ethylene oxidase plant hormone / PLANT PROTEIN
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-AMINOCYCLOBUTANECARBOXLIC ACID / : / aminocyclopropanecarboxylate oxidase
Similarity search - Component
Biological speciesAmborella trichopoda (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: aminocyclopropanecarboxylate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1313
Polymers35,9601
Non-polymers1712
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-13 kcal/mol
Surface area14630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.381, 57.813, 113.913
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

-
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-192 / 1-AMINOCYCLOBUTANECARBOXLIC ACID


Type: peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.07 %
Description: Gold bar shaped, size rarious up to 0.5 millimeter.
Crystal growTemperature: 295.15 K / Method: evaporation / pH: 9.5
Details: Anaerobic condition. 25-28% PEG3350, 0.1 M CHES pH9.5. 3 mM ammonium iron (II) hexahydrate, 30 mM 1-aminocyclobutane-1-carboxylic acid. Microseeding.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.78338 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.78338 Å / Relative weight: 1
ReflectionResolution: 1.8→40.6 Å / Num. obs: 27356 / % possible obs: 99.9 % / Redundancy: 12.1 % / Biso Wilson estimate: 22.45 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.058 / Rrim(I) all: 0.149 / Net I/σ(I): 9.5
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 1.482 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1558 / CC1/2: 0.774 / Rpim(I) all: 0.429 / Rrim(I) all: 1.545 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→40.57 Å / SU ML: 0.234 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.6373
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2295 1322 4.85 %
Rwork0.1958 25908 -
obs0.1974 27230 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.49 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2445 0 9 139 2593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072519
X-RAY DIFFRACTIONf_angle_d0.8653400
X-RAY DIFFRACTIONf_chiral_restr0.0522362
X-RAY DIFFRACTIONf_plane_restr0.0073441
X-RAY DIFFRACTIONf_dihedral_angle_d13.6091958
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.870.44711420.34152782X-RAY DIFFRACTION97.6
1.87-1.960.28981490.26582822X-RAY DIFFRACTION99.53
1.96-2.060.29481450.23282847X-RAY DIFFRACTION99.6
2.06-2.190.25371350.21932847X-RAY DIFFRACTION99.73
2.19-2.360.25241440.18582850X-RAY DIFFRACTION99.73
2.36-2.590.23931500.18292892X-RAY DIFFRACTION99.84
2.59-2.970.25611510.18512852X-RAY DIFFRACTION98.75
2.97-3.740.18751490.17742938X-RAY DIFFRACTION99.97
3.74-40.570.18751570.17783078X-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)
11.335330211850.1830155945470.08463516695931.479164773530.1392281809821.136267074050.0761149355416-0.09939393191820.0785408395115-0.046682462028-0.0455392033528-0.0275727010712-0.05087421895910.0412236685698-0.03748378222490.1497441467560.01226670709510.009649838931650.354279082522-0.0253238275760.142398753492-4.43304318614-1.1882531085312.4205347629
22.732051235740.293412777673.222534461045.078160420952.30103952985.113573098870.0804974407762-0.5034101236080.08685849944890.124312592803-0.0514458500670.201939441770.0761832746079-0.178053701237-0.01518017935870.231404225503-0.0279124453410.03546412608110.552037832177-0.04268547497310.228852497841-1.107186441026.4984253658128.0049978861
31.300374679331.12897800034-0.2162563269894.46508406180.94078467923.299221862130.1092717149480.5721023662960.328758746594-0.681336704436-0.0392469802258-0.171407189431-0.466877775166-0.0564539497956-0.06731367797450.2536141898430.04896817088710.006345629472120.3846209157020.05336227390280.185159108813-6.428243871054.0335286002-1.54001070806
45.044057138311.08876025719-3.893858532053.68305939113-1.45208306317.526551130560.0499541977118-0.464208945133-0.4532473325020.2924870510710.09509427421070.293183713910.527744494962-0.132055899254-0.1140675073580.2228014786850.00680065028763-0.03514127294940.3872005435630.0569967682390.306396332081-12.5700718677-21.414078088515.5023112479
51.489921870541.150156733550.009997833817153.36570855047-0.6418846093081.44093144946-0.0163657103791-0.550433349062-0.1845813186240.231338547630.089158197388-0.0782211481970.09562870221590.00741450464002-0.08292652763040.2432039671190.0290698731111-0.03391368508620.5288175679530.04974488979030.198454653566-4.39965738239-15.778277330820.310004935
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 108 through 278 )108 - 278102 - 272
22chain 'A' and (resid 279 through 310 )279 - 310273 - 304
33chain 'A' and (resid 2 through 43 )2 - 431 - 42
44chain 'A' and (resid 44 through 75 )44 - 7543 - 74
55chain 'A' and (resid 76 through 107 )76 - 10775 - 101

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more