[English] 日本語
Yorodumi
- PDB-7rom: Crystal structure of Saccharomyces cerevisiae NADH-cytochrome b5 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rom
TitleCrystal structure of Saccharomyces cerevisiae NADH-cytochrome b5 reductase 1 (Cbr1) fragment (residues 28-284) bound to FAD
ComponentsNADH-cytochrome b5 reductase 1
KeywordsOXIDOREDUCTASE / Reductase / electron transfer
Function / homology
Function and homology information


Vitamin C (ascorbate) metabolism / cytochrome-b5 reductase / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / cytochrome-b5 reductase activity, acting on NAD(P)H / protein histidyl modification to diphthamide / Platelet degranulation / NADH dehydrogenase activity / Neutrophil degranulation / mitochondrial outer membrane / membrane => GO:0016020 ...Vitamin C (ascorbate) metabolism / cytochrome-b5 reductase / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / cytochrome-b5 reductase activity, acting on NAD(P)H / protein histidyl modification to diphthamide / Platelet degranulation / NADH dehydrogenase activity / Neutrophil degranulation / mitochondrial outer membrane / membrane => GO:0016020 / endoplasmic reticulum membrane / mitochondrion / nucleus / plasma membrane
Similarity search - Function
NADH:cytochrome b5 reductase-like / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Flavoprotein pyridine nucleotide cytochrome reductase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / TRIETHYLENE GLYCOL / NADH-cytochrome b5 reductase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsFenwick, M.K. / Zhang, Y. / Lin, H.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK107868-04 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124165-01 United States
National Institutes of Health/Office of the DirectorS10OD021527 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: To Be Published
Title: Crystal structure of Saccharomyces cerevisiae NADH-cytochrome b5 reductase 1 (Cbr1) fragment (residues 28-284) bound to FAD
Authors: Fenwick, M.K. / Lin, H.
History
DepositionJul 31, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NADH-cytochrome b5 reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2227
Polymers29,0301
Non-polymers1,1926
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.225, 72.225, 114.669
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein NADH-cytochrome b5 reductase 1 / Microsomal cytochrome b reductase / P35


Mass: 29029.584 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CBR1, CBR, CBR5, YIL043C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P38626, cytochrome-b5 reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 435 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion / Details: 20 % (w/v) PEG 3350 and 200 mM sodium thiocyanate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97903 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 1.65→46.65 Å / Num. obs: 36978 / % possible obs: 99.6 % / Redundancy: 8.7 % / Biso Wilson estimate: 23.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.018 / Rrim(I) all: 0.055 / Net I/σ(I): 21.7 / Num. measured all: 322326 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.65-1.688.90.5761621618160.870.2030.6123.5100
9.04-46.657.40.03219622640.9990.0120.03448.296

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EIX

2eix


Resolution: 1.65→46.65 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1881 1839 4.98 %
Rwork0.1553 35110 -
obs0.1569 36949 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.12 Å2 / Biso mean: 26.8104 Å2 / Biso min: 12.06 Å2
Refinement stepCycle: final / Resolution: 1.65→46.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1983 0 76 435 2494
Biso mean--21.75 38.3 -
Num. residues----255
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.690.26341370.215726562793100
1.69-1.740.25171450.202126562801100
1.74-1.80.33031150.243727132828100
1.8-1.870.30521440.222926532797100
1.87-1.940.21081430.179126842827100
1.94-2.030.19191370.163826802817100
2.03-2.140.21521630.170826722835100
2.14-2.270.20531210.17332705282699
2.27-2.440.18911490.15582685283499
2.44-2.690.19461410.15362718285999
2.69-3.080.17551550.15432703285899
3.08-3.880.16691500.13292727287798
3.88-46.650.15131390.13292858299796
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)
12.60171.1208-0.92815.0305-1.38741.41680.00170.20370.1837-0.28850.1645-0.0222-0.11920.0632-0.17470.16-0.03270.01020.1872-0.04470.192238.956512.866635.5167
21.5768-1.144-0.022.02630.25230.8490.00720.06790.1337-0.02070.0479-0.2623-0.11270.183-0.05290.1656-0.02460.01410.1593-0.00760.135334.56619.887734.3352
31.0067-1.0591.08113.5337-2.29223.1694-0.0489-0.05520.0410.18320.06340.0279-0.1426-0.038-0.01260.14010.00340.01390.1199-0.01340.13319.604310.090748.0388
41.93130.56220.08143.3618-2.62444.6511-0.07470.1754-0.0494-0.22010.17610.27060.3506-0.3292-0.06690.1843-0.03850.0020.1342-0.01630.205312.3185-0.574738.0388
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 61 )A30 - 61
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 147 )A62 - 147
3X-RAY DIFFRACTION3chain 'A' and (resid 148 through 223 )A148 - 223
4X-RAY DIFFRACTION4chain 'A' and (resid 224 through 284 )A224 - 284

+
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