[English] 日本語
Yorodumi
- PDB-4o6y: Crystal Structure of Cytochrome b561 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4o6y
TitleCrystal Structure of Cytochrome b561
ComponentsProbable transmembrane ascorbate ferrireductase 2
KeywordsOXIDOREDUCTASE / alpha helical membrane protein / ascorbate-dependent oxidoreductase
Function / homology
Function and homology information


ascorbate ferrireductase (transmembrane) / ferric-chelate reductase activity / 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
PROTOPORPHYRIN IX CONTAINING FE / Transmembrane ascorbate ferrireductase 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 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 1.2Mar 20, 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_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 / _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: Probable transmembrane ascorbate ferrireductase 2
B: Probable transmembrane ascorbate ferrireductase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1827
Polymers50,6202
Non-polymers2,5625
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint-128 kcal/mol
Surface area18480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.275, 108.514, 110.785
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 / Heme B


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.18 Å3/Da / Density % sol: 43.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30% PEG400, 0.4M Li2SO4, 0.1M 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, 2013
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: 1.7→40 Å / Num. all: 48888 / Num. obs: 48448 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 27.54 Å2
Reflection shellResolution: 1.7→1.76 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→27.128 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8633 / SU ML: 0.12 / σ(F): 1.34 / Phase error: 20.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2447 5.05 %Random
Rwork0.2015 ---
obs0.2022 48440 99.1 %-
all-48888 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.747 Å2 / ksol: 0.431 e/Å3
Displacement parametersBiso max: 89.15 Å2 / Biso mean: 36.3506 Å2 / Biso min: 19.89 Å2
Baniso -1Baniso -2Baniso -3
1-8.048 Å2-0 Å20 Å2
2---8.1369 Å20 Å2
3---0.0889 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3297 0 177 76 3550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143588
X-RAY DIFFRACTIONf_angle_d1.5244941
X-RAY DIFFRACTIONf_chiral_restr0.069553
X-RAY DIFFRACTIONf_plane_restr0.005569
X-RAY DIFFRACTIONf_dihedral_angle_d15.2621171
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6997-1.73440.26661360.26032523265994
1.7344-1.77210.24671250.249827182843100
1.7721-1.81330.25821440.220726992843100
1.8133-1.85870.22861300.216527202850100
1.8587-1.90890.23941500.208426982848100
1.9089-1.96510.23361510.208326882839100
1.9651-2.02850.18871400.195827122852100
2.0285-2.10090.21951520.19327092861100
2.1009-2.1850.18241290.183727142843100
2.185-2.28440.22871430.18327112854100
2.2844-2.40480.1881580.173727152873100
2.4048-2.55540.22181370.178327212858100
2.5554-2.75250.20841350.178627632898100
2.7525-3.02920.1851550.188627312886100
3.0292-3.46670.20371620.207427362898100
3.4667-4.36470.21341550.19142756291199
4.3647-27.13190.24061450.23372679282492
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)
11.8322-1.0078-0.49662.24850.18011.57190.10060.1669-0.02-0.268-0.10040.0834-0.0957-0.1365-0.00210.1937-0.0041-0.01940.2332-0.02540.1909-10.683-25.50419.3267
21.59380.0046-0.30712.1552-0.15462.119-0.0661-0.2381-0.00290.19280.0681-0.00980.0066-0.07010.00290.19690.0257-0.01770.2439-0.02110.1768-14.1869-22.784344.2274
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

+
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