[English] 日本語
Yorodumi
- PDB-9plv: X-ray crystal structure of the beta-carotene oxygenase like g (BC... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9plv
TitleX-ray crystal structure of the beta-carotene oxygenase like g (BCOLg) from Lancelet floridae
ComponentsBeta-carotene oxygenase like g (BCOLg)
KeywordsOXIDOREDUCTASE / Beta-carotene oxygenase like g (BCOLg) / non-heme iron-containing oxygenase / Branchiostoma / Lancelet
Function / homologyCarotenoid oxygenase / Retinal pigment epithelial membrane protein / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / metal ion binding / ACETATE ION / Chem-ETE / : / DI(HYDROXYETHYL)ETHER / Uncharacterized protein
Function and homology information
Biological speciesBranchiostoma floridae (Florida lancelet)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsUppal, S. / Govindarajan, G. / Poliakov, E. / Gittis, A. / Garboczi, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI) United States
CitationJournal: To Be Published
Title: X-ray crystal structure of the beta-carotene oxygenase like g (BCOLg) from Lancelet floridae
Authors: Uppal, S. / Govindarajan, G. / Muslinkina, L. / Herrera, G. / Poliakov, E. / Gittis, A. / Garboczi, D. / Redmond, T.M.
History
DepositionJul 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-carotene oxygenase like g (BCOLg)
B: Beta-carotene oxygenase like g (BCOLg)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,52660
Polymers127,8232
Non-polymers5,70358
Water4,882271
1
A: Beta-carotene oxygenase like g (BCOLg)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,94031
Polymers63,9111
Non-polymers3,02930
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-carotene oxygenase like g (BCOLg)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,58629
Polymers63,9111
Non-polymers2,67428
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.460, 139.910, 93.760
Angle α, β, γ (deg.)90.000, 98.264, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Beta-carotene oxygenase like g (BCOLg)


Mass: 63911.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Branchiostoma floridae (Florida lancelet)
Gene: BRAFLDRAFT_81327 / Production host: Mammalia (mammals) / References: UniProt: C3YQV9

-
Sugars , 2 types, 8 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 8 types, 321 molecules

#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O5
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.7 % / Description: Chunk
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Condition 22 of Crystal Screen (Hampton Research, HR2-110) supplemented with 5% ethylene glycol.
PH range: 7.4 - 8.5

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: DECTRIS EIGER2 R 4M / Detector: PIXEL / Date: Dec 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.4→24.85 Å / Num. obs: 48073 / % possible obs: 98.1 % / Redundancy: 4.25 % / Biso Wilson estimate: 33.38 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.101 / Net I/σ(I): 11.98
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 3.04 % / Mean I/σ(I) obs: 2.82 / Num. unique obs: 3240 / CC1/2: 0.847 / Rrim(I) all: 0.393 / % possible all: 89.6

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→24.56 Å / SU ML: 0.281 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.0223
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2242 2000 4.16 %
Rwork0.1753 46073 -
obs0.1774 48073 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.65 Å2
Refinement stepCycle: LAST / Resolution: 2.4→24.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7603 0 365 271 8239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00788173
X-RAY DIFFRACTIONf_angle_d1.020911077
X-RAY DIFFRACTIONf_chiral_restr0.0581255
X-RAY DIFFRACTIONf_plane_restr0.00791412
X-RAY DIFFRACTIONf_dihedral_angle_d12.87312994
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.2821300.22312986X-RAY DIFFRACTION89.44
2.46-2.530.31971400.21043238X-RAY DIFFRACTION96.9
2.53-2.60.26531450.20783332X-RAY DIFFRACTION99.94
2.6-2.680.28441450.20813353X-RAY DIFFRACTION99.94
2.68-2.780.25741430.20543297X-RAY DIFFRACTION99.91
2.78-2.890.25071460.19443351X-RAY DIFFRACTION99.94
2.89-3.020.24161450.19763351X-RAY DIFFRACTION99.83
3.02-3.180.23381440.19383319X-RAY DIFFRACTION99.31
3.18-3.380.25671440.18183334X-RAY DIFFRACTION99.2
3.38-3.640.21471440.17283291X-RAY DIFFRACTION98.34
3.64-4.010.1921420.16023290X-RAY DIFFRACTION97.75
4.01-4.580.17341410.13953266X-RAY DIFFRACTION97.37
4.58-5.760.18941450.14193335X-RAY DIFFRACTION98.44
5.76-24.560.22251460.18013330X-RAY DIFFRACTION97.75

+
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