[English] 日本語
Yorodumi
- PDB-4ou9: Crystal structure of apocarotenoid oxygenase in the presence of T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ou9
TitleCrystal structure of apocarotenoid oxygenase in the presence of Triton X-100
ComponentsApocarotenoid-15,15'-oxygenase
KeywordsOXIDOREDUCTASE / monotopic membrane protein / non-heme iron / metalloenzyme / 4-His iron center / beta propeller / carotenoid oxygenase
Function / homologyall-trans-8'-apo-beta-carotenal 15,15'-oxygenase / all-trans-8'-apo-beta-carotenal 15,15'-oxygenase activity / carotenoid dioxygenase activity / carotene catabolic process / Carotenoid oxygenase / Retinal pigment epithelial membrane protein / metal ion binding / : / Apocarotenoid-15,15'-oxygenase
Function and homology information
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsSui, X. / Palczewski, K. / Kiser, P.D.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Analysis of Carotenoid Isomerase Activity in a Prototypical Carotenoid Cleavage Enzyme, Apocarotenoid Oxygenase (ACO).
Authors: Sui, X. / Kiser, P.D. / Che, T. / Carey, P.R. / Golczak, M. / Shi, W. / von Lintig, J. / Palczewski, K.
History
DepositionFeb 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2May 21, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Apocarotenoid-15,15'-oxygenase
B: Apocarotenoid-15,15'-oxygenase
C: Apocarotenoid-15,15'-oxygenase
D: Apocarotenoid-15,15'-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,67110
Polymers217,3774
Non-polymers2946
Water15,763875
1
A: Apocarotenoid-15,15'-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4353
Polymers54,3441
Non-polymers912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Apocarotenoid-15,15'-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4353
Polymers54,3441
Non-polymers912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Apocarotenoid-15,15'-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4002
Polymers54,3441
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Apocarotenoid-15,15'-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4002
Polymers54,3441
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.470, 125.390, 202.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Apocarotenoid-15,15'-oxygenase / ACO / 8'-apo-beta-carotenal 15 / 15'-oxygenase / Diox1


Mass: 54344.191 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: Diox1, sll1541 / Production host: Escherichia coli (E. coli)
References: UniProt: P74334, all-trans-8'-apo-beta-carotenal 15,15'-oxygenase
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 875 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.45 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 3350, NH4Cl, Triton X-100, BTP, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 281K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 10, 2013
RadiationMonochromator: Silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 203162 / Num. obs: 200469 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3

-
Processing

Software
NameClassification
XDSdata scaling
REFMACrefinement
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→48.61 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 8.364 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20467 9860 4.9 %RANDOM
Rwork0.17717 ---
obs0.17849 190607 98.67 %-
all-203162 --
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.673 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å2-0 Å2-0 Å2
2--0.56 Å2-0 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2→48.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15098 0 6 875 15979
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01915616
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214528
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.95421287
X-RAY DIFFRACTIONr_angle_other_deg0.746333471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58551932
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04823.836743
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.048152401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3841593
X-RAY DIFFRACTIONr_chiral_restr0.0860.22247
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02117986
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023747
X-RAY DIFFRACTIONr_mcbond_it1.6912.6057707
X-RAY DIFFRACTIONr_mcbond_other1.6912.6057706
X-RAY DIFFRACTIONr_mcangle_it2.5543.8969637
X-RAY DIFFRACTIONr_mcangle_other2.5543.8979638
X-RAY DIFFRACTIONr_scbond_it2.2222.8927909
X-RAY DIFFRACTIONr_scbond_other2.2222.8927909
X-RAY DIFFRACTIONr_scangle_other3.5734.22611647
X-RAY DIFFRACTIONr_long_range_B_refined5.24221.37717440
X-RAY DIFFRACTIONr_long_range_B_other5.22921.34717375
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 742 -
Rwork0.29 14104 -
obs--99.78 %
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)
11.27950.3031-0.32311.5175-0.39111.73580.07780.04260.0131-0.1642-0.0874-0.08050.0451-0.09230.00960.20810.04070.02270.02140.00940.006324.46891.141992.0547
21.4372-0.199-0.60261.40240.49761.6491-0.11650.0826-0.0190.07720.06730.0830.0777-0.03990.04920.2165-0.02830.02670.0194-0.00190.008331.13094.854341.3926
31.2288-0.5858-0.25341.45680.23861.7023-0.0344-0.0288-0.16090.034-0.05070.19840.0967-0.14590.08510.18640.01890.01110.0344-0.00090.094444.0392-44.082885.5048
41.87310.8153-0.03061.490.01881.329-0.12360.12090.2057-0.12970.14540.1879-0.1647-0.0204-0.02180.2731-0.0605-0.01010.02680.02830.0937-12.9716-17.584435.2633
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 848
2X-RAY DIFFRACTION2B10 - 824
3X-RAY DIFFRACTION3C12 - 809
4X-RAY DIFFRACTION4D12 - 794

+
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