[English] 日本語
Yorodumi
- PDB-5zlg: Human duodenal cytochrome b (Dcytb) in zinc ion and ascorbate bou... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zlg
TitleHuman duodenal cytochrome b (Dcytb) in zinc ion and ascorbate bound form
ComponentsCytochrome b reductase 1
KeywordsOXIDOREDUCTASE / electron transport
Function / homology
Function and homology information


transmembrane monodehydroascorbate reductase activity / ascorbate homeostasis / ascorbate ferrireductase (transmembrane) / transmembrane ascorbate ferrireductase activity / reductive iron assimilation / : / oxidoreductase activity, acting on metal ions / response to iron ion / brush border membrane / Iron uptake and transport ...transmembrane monodehydroascorbate reductase activity / ascorbate homeostasis / ascorbate ferrireductase (transmembrane) / transmembrane ascorbate ferrireductase activity / reductive iron assimilation / : / oxidoreductase activity, acting on metal ions / response to iron ion / brush border membrane / Iron uptake and transport / intracellular iron ion homeostasis / oxidoreductase activity / apical plasma membrane / lysosomal membrane / extracellular exosome / membrane / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
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.
Similarity search - Domain/homology
ASCORBIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Plasma membrane ascorbate-dependent reductase CYBRD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
Model detailsAscorbate-dependent ferric reductase Dcytb
AuthorsGanasen, M. / Togashi, H. / Mauk, G.A. / Shiro, Y. / Sawai, H. / Sugimoto, H.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP26220807 Japan
Japan Society for the Promotion of ScienceJP24687015 Japan
Japan Society for the Promotion of ScienceJP25871213 Japan
CitationJournal: Commun Biol / Year: 2018
Title: Structural basis for promotion of duodenal iron absorption by enteric ferric reductase with ascorbate.
Authors: Ganasen, M. / Togashi, H. / Takeda, H. / Asakura, H. / Tosha, T. / Yamashita, K. / Hirata, K. / Nariai, Y. / Urano, T. / Yuan, X. / Hamza, I. / Mauk, A.G. / Shiro, Y. / Sugimoto, H. / Sawai, H.
History
DepositionMar 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rrim_I_all
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Category: chem_comp / struct_site / struct_site_gen / Item: _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 22, 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: Cytochrome b reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0136
Polymers32,3621
Non-polymers1,6515
Water543
1
A: Cytochrome b reductase 1
hetero molecules

A: Cytochrome b reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,02512
Polymers64,7242
Non-polymers3,30110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area9920 Å2
ΔGint-199 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.180, 115.570, 48.600
Angle α, β, γ (deg.)90.000, 118.440, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Cytochrome b reductase 1 / Duodenal cytochrome b / Ferric-chelate reductase 3


Mass: 32362.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYBRD1, DCYTB, FRRS3 / Plasmid: pET-21b / Production host: Escherichia coli BL21 Star (DE3) (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: Q53TN4, Oxidoreductases
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Sugar ChemComp-ASC / ASCORBIC ACID / Vitamin C / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O6 / Comment: medication*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.48 Å3/Da / Density % sol: 50.33 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.5 / Details: 20%(v/v) Jeffamine ED-2003, 0.1 M HEPES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 14, 2016 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→43.114 Å / Num. obs: 7824 / % possible obs: 99.3 % / Redundancy: 49.585 % / Biso Wilson estimate: 30.86 Å2 / CC1/2: 0.967 / Rmerge(I) obs: 1.608 / Rrim(I) all: 0.01624 / Χ2: 1.325 / Net I/σ(I): 8.47 / Num. measured all: 387956 / Scaling rejects: 454
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.8-2.9748.80721.5111.0361790127012660.48121.73399.7
2.97-3.1749.1685.2461.6856936116711580.7155.29999.2
3.17-3.4349.0153.2822.6255142112611250.8513.31599.9
3.43-3.7646.6591.5674.547732103110230.9361.58399.2
3.76-4.250.2850.7538.91460619209160.9720.7699.6
4.2-4.8552.5340.55115.04426588238120.9840.55698.7
4.85-5.9351.4130.41417.44349616836800.9920.41899.6
5.93-8.3747.1330.36322.2255935515430.9950.36698.5
8.37-43.11456.7540.32737.04170833073010.9970.32998

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O7G
Resolution: 2.8→43.114 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2525 381 4.87 %
Rwork0.2057 7440 -
obs0.208 7821 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.51 Å2 / Biso mean: 35.1293 Å2 / Biso min: 6.4 Å2
Refinement stepCycle: final / Resolution: 2.8→43.114 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1789 0 111 3 1903
Biso mean--30.93 18.21 -
Num. residues----225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091989
X-RAY DIFFRACTIONf_angle_d1.2482743
X-RAY DIFFRACTIONf_chiral_restr0.048301
X-RAY DIFFRACTIONf_plane_restr0.006320
X-RAY DIFFRACTIONf_dihedral_angle_d13.8851076
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7998-2.89980.3045340.29751785100
2.8998-3.01590.3491390.2524746785100
3.0159-3.15310.2992390.2201741780100
3.1531-3.31930.3047420.2251731773100
3.3193-3.52720.2403330.2039745778100
3.5272-3.79930.2133350.1876747782100
3.7993-4.18140.2027410.1669731772100
4.1814-4.78580.2968370.199374678399
4.7858-6.0270.2836400.215750790100
6.027-43.11880.1596410.1738752793100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.1639-0.4106-1.46051.8752-0.31453.3446-0.12350.322-0.2546-0.2227-0.02950.07370.3249-0.2460.17140.3873-0.01930.18680.2885-0.0340.184925.208528.99724.1053
22.155-0.12140.08180.71130.50810.86670.07450.18620.2229-0.4902-0.1017-0.183-0.4507-0.097-0.01210.48410.19060.04340.19080.01470.099520.324944.21385.0101
31.9486-0.7917-0.34312.1696-0.45231.56260.09270.3131-0.3917-0.3626-0.15160.2842-0.1298-0.40420.0270.15340.12660.00160.2473-0.05630.16359.408731.77159.4858
40.611-0.9747-0.62523.48520.78113.13540.06280.17280.1309-0.4361-0.13330.6212-0.5513-0.60030.09940.9510.4905-0.02850.76250.08660.5052.386753.87910.3756
50.945-0.0867-0.1180.22170.01190.4890.05530.1136-0.0897-0.05840.0166-0.0333-0.074-0.02460.24040.09330.00850.11030.023-0.00650.139117.804232.216216.8957
60.8509-0.2214-0.55680.79150.131.23870.0454-0.0326-0.0241-0.067-0.0512-0.0268-0.1770.0492-0.07320.229-0.04160.14240.14530.0470.119127.37235.423613.5425
74.3671-0.6425-2.012.7736-0.78982.3819-0.00020.0616-0.1317-0.0287-0.02040.10120.0097-0.12950.08780.11720.04450.08560.2666-0.04380.204314.397523.244913.3644
81.29560.15470.14714.05441.68953.9360.02630.10010.1303-0.5738-0.12650.2101-0.5531-0.24420.09690.45820.1311-0.04580.2779-0.09240.185712.887748.4989.8889
93.06851.48051.36053.45912.35278.58260.55840.131-1.4759-0.6603-0.32390.53260.96930.4244-0.23290.44780.1868-0.11130.746-0.23580.521515.569413.663812.7476
108.68712.16921.08882.30913.11528.35830.0414-0.26760.47110.1016-0.0759-0.0283-0.6781-0.09040.0370.79030.08710.00280.49980.19730.77539.392557.062210.2902
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 6:51)A6 - 51
2X-RAY DIFFRACTION2(chain A and resid 52:77)A52 - 77
3X-RAY DIFFRACTION3(chain A and resid 78:138)A78 - 138
4X-RAY DIFFRACTION4(chain A and resid 139:155)A139 - 155
5X-RAY DIFFRACTION5(chain A and resid 156:186)A156 - 186
6X-RAY DIFFRACTION6(chain A and resid 187:230)A187 - 230
7X-RAY DIFFRACTION7(chain A and resid 401)A401
8X-RAY DIFFRACTION8(chain A and resid 402)A402
9X-RAY DIFFRACTION9(chain A and resid 403:404)A403 - 404
10X-RAY DIFFRACTION10(chain A and resid 405)A405

+
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