[English] 日本語
Yorodumi
- PDB-4o79: Crystal Structure of Ascorbate-bound Cytochrome b561, crystal soa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4o79
TitleCrystal Structure of Ascorbate-bound Cytochrome b561, crystal soaked in 1 M L-ascorbate for 10 minutes
ComponentsProbable transmembrane ascorbate ferrireductase 2
KeywordsOXIDOREDUCTASE / alpha helical membrane protein / ascorbate-dependent oxidoreductase
Function / homology
Function and homology information


ferric-chelate reductase activity / ascorbate ferrireductase (transmembrane) / transmembrane ascorbate ferrireductase activity / L-ascorbic acid metabolic process / Golgi apparatus / membrane / metal ion binding
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1770 / Cytochrome b561/ferric reductase transmembrane / Cytochrome b561/Cytochrome b reductase 1-like / Eukaryotic cytochrome b561 / Cytochrome b561 domain profile. / Cytochrome b-561 / ferric reductase transmembrane domain. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ASCORBIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Transmembrane ascorbate ferrireductase 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.003 Å
AuthorsLu, P. / Ma, D. / Yan, C. / Gong, X. / Du, M. / Shi, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure and mechanism of a eukaryotic transmembrane ascorbate-dependent oxidoreductase
Authors: Lu, P. / Ma, D. / Yan, C. / Gong, X. / Du, M. / Shi, Y.
History
DepositionDec 24, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references / Non-polymer description
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable transmembrane ascorbate ferrireductase 2
B: Probable transmembrane ascorbate ferrireductase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3588
Polymers50,6202
Non-polymers2,7386
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-125 kcal/mol
Surface area18240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.193, 108.648, 111.389
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein Probable transmembrane ascorbate ferrireductase 2 / Cytochrome b561-1 / Artb561-2 / AtCytb561


Mass: 25310.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CYB561B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SWS1, EC: 1.16.5.1
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Sugar ChemComp-ASC / ASCORBIC ACID / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O6 / Comment: medication*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30% PEG400, 400mM Li2SO4, 100 mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 30170 / Num. obs: 29506 / % possible obs: 97.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 33.72 Å2
Reflection shellResolution: 2→2.07 Å / % possible all: 87

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4O6Y

4o6y


Resolution: 2.003→30.585 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8514 / SU ML: 0.15 / σ(F): 1.34 / Phase error: 21.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 1499 5.08 %RANDOM
Rwork0.2017 ---
obs0.2023 29496 97.55 %-
all-30170 --
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 119.63 Å2 / Biso mean: 43.8759 Å2 / Biso min: 22.12 Å2
Baniso -1Baniso -2Baniso -3
1-6.178 Å20 Å2-0 Å2
2---9.7047 Å2-0 Å2
3---3.5267 Å2
Refinement stepCycle: LAST / Resolution: 2.003→30.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3297 0 189 66 3552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083600
X-RAY DIFFRACTIONf_angle_d1.1334958
X-RAY DIFFRACTIONf_chiral_restr0.063555
X-RAY DIFFRACTIONf_plane_restr0.004572
X-RAY DIFFRACTIONf_dihedral_angle_d14.941178
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0031-2.06770.29541170.27742180229785
2.0677-2.14160.26981340.24532436257095
2.1416-2.22730.2641320.234425832715100
2.2273-2.32870.22921250.208625982723100
2.3287-2.45140.22351440.186725722716100
2.4514-2.60490.19281340.185525942728100
2.6049-2.80590.18081380.177525882726100
2.8059-3.0880.21851460.187925942740100
3.088-3.53430.21791430.188926062749100
3.5343-4.45070.19021520.18222607275999
4.4507-30.58810.21481340.22312639277395
Refinement TLS params.Method: refined / Origin x: 12.4521 Å / Origin y: 24.2453 Å / Origin z: -23.5938 Å
111213212223313233
T0.2454 Å2-0.021 Å20.0179 Å2-0.2878 Å20.044 Å2--0.2867 Å2
L1.1504 °2-0.3579 °20.297 °2-1.2073 °2-0.2294 °2--1.3191 °2
S0.0211 Å °0.0267 Å °-0.03 Å °0.0031 Å °-0.0377 Å °0.021 Å °0.0513 Å °0.0546 Å °0 Å °
Refinement TLS groupSelection details: ALL

+
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://pdbjlvh1.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