[English] 日本語
Yorodumi
- PDB-5n0j: Structure of a novel oxidoreductase from Gloeobacter violaceus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5n0j
TitleStructure of a novel oxidoreductase from Gloeobacter violaceus
ComponentsGll2934 protein
KeywordsOXIDOREDUCTASE / flavoprotein
Function / homology: / thioredoxin-disulfide reductase (NADPH) activity / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / cell redox homeostasis / FAD/NAD(P)-binding domain superfamily / nucleotide binding / FLAVIN-ADENINE DINUCLEOTIDE / Gll2934 protein
Function and homology information
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.949 Å
AuthorsBuey, R.M. / Galindo-Trigo, S. / de Pereda, J.M. / Balsera, M.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Unprecedented pathway of reducing equivalents in a diflavin-linked disulfide oxidoreductase.
Authors: Buey, R.M. / Arellano, J.B. / Lopez-Maury, L. / Galindo-Trigo, S. / Velazquez-Campoy, A. / Revuelta, J.L. / de Pereda, J.M. / Florencio, F.J. / Schurmann, P. / Buchanan, B.B. / Balsera, M.
History
DepositionFeb 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gll2934 protein
B: Gll2934 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,25021
Polymers77,6672
Non-polymers4,58319
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12730 Å2
ΔGint-210 kcal/mol
Surface area24990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.842, 143.325, 265.111
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein Gll2934 protein


Mass: 38833.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Strain: PCC 7421 / Gene: gll2934 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NCP4
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 3.54 Å3/Da / Density % sol: 65.23 %
Description: Crystals were yellow but turned transparent after soaking them in a solution with 0.1 M reduced glutathione for a few minutes (up to 5 minutes)
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 1.5 M Li2SO4 0.1 M HEPES, pH 7.5 Crystals were soaked for 5 min in a solution of mother liquor plus 0.1 M reduced Glutathione, immersed in a solution of mother liquor containing 25% Ethylene ...Details: 1.5 M Li2SO4 0.1 M HEPES, pH 7.5 Crystals were soaked for 5 min in a solution of mother liquor plus 0.1 M reduced Glutathione, immersed in a solution of mother liquor containing 25% Ethylene glycol and immediately flash-frozen in liquid nitrogen

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.99989 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99989 Å / Relative weight: 1
ReflectionResolution: 1.949→49.73 Å / Num. obs: 80406 / % possible obs: 99.03 % / Redundancy: 10 % / CC1/2: 0.997 / Rmerge(I) obs: 0.17 / Net I/σ(I): 9.19
Reflection shellResolution: 1.949→2.019 Å / Redundancy: 10 % / Rmerge(I) obs: 2.84 / Mean I/σ(I) obs: 0.88 / CC1/2: 0.472 / % possible all: 95.71

-
Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JRI

5jri


Resolution: 1.949→49.728 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 3961 4.94 %
Rwork0.2017 --
obs0.2033 80159 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.949→49.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4679 0 287 341 5307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115135
X-RAY DIFFRACTIONf_angle_d1.1057036
X-RAY DIFFRACTIONf_dihedral_angle_d13.9712824
X-RAY DIFFRACTIONf_chiral_restr0.061777
X-RAY DIFFRACTIONf_plane_restr0.007849
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9487-1.97250.47311450.4622433X-RAY DIFFRACTION90
1.9725-1.99740.461490.43532669X-RAY DIFFRACTION98
1.9974-2.02370.43241270.39722675X-RAY DIFFRACTION98
2.0237-2.05150.39361430.36722686X-RAY DIFFRACTION99
2.0515-2.08080.37391530.35432684X-RAY DIFFRACTION100
2.0808-2.11180.32011500.32412688X-RAY DIFFRACTION100
2.1118-2.14480.35231300.31462739X-RAY DIFFRACTION99
2.1448-2.180.34721320.30462695X-RAY DIFFRACTION100
2.18-2.21760.33741590.28372718X-RAY DIFFRACTION100
2.2176-2.25790.31121500.2752688X-RAY DIFFRACTION100
2.2579-2.30130.28951290.26572729X-RAY DIFFRACTION100
2.3013-2.34830.29751440.25212751X-RAY DIFFRACTION100
2.3483-2.39940.25661470.23932700X-RAY DIFFRACTION100
2.3994-2.45520.28561370.22162709X-RAY DIFFRACTION100
2.4552-2.51660.26671480.2122776X-RAY DIFFRACTION100
2.5166-2.58460.22141430.2072667X-RAY DIFFRACTION100
2.5846-2.66070.25421430.2062718X-RAY DIFFRACTION99
2.6607-2.74650.25021340.19432770X-RAY DIFFRACTION100
2.7465-2.84470.22991430.18732724X-RAY DIFFRACTION100
2.8447-2.95860.20441330.19292744X-RAY DIFFRACTION100
2.9586-3.09320.24051330.18892744X-RAY DIFFRACTION100
3.0932-3.25620.21561370.18062782X-RAY DIFFRACTION100
3.2562-3.46020.19461210.17272760X-RAY DIFFRACTION99
3.4602-3.72730.21161600.15752726X-RAY DIFFRACTION99
3.7273-4.10220.17081570.14462752X-RAY DIFFRACTION99
4.1022-4.69540.17231510.13252772X-RAY DIFFRACTION99
4.6954-5.91420.18221380.16382788X-RAY DIFFRACTION98
5.9142-49.74460.23861250.22542911X-RAY DIFFRACTION97
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)
11.3936-0.1512-0.73730.85860.65250.9804-0.0605-0.53870.12650.18710.1081-0.16460.25250.40270.00120.44650.0444-0.04020.6671-0.12180.411778.5836161.6015307.4263
21.39220.16420.21990.89430.61271.26960.0106-0.05610.08880.0627-0.0002-0.03040.06740.11940.00040.3845-0.0107-0.00070.2864-0.07030.361474.686154.9276276.6846
30.7479-0.2763-0.16540.54620.70041.2704-0.0968-0.371-0.02630.16130.01440.03650.31720.17930.01490.44830.0157-0.00340.5018-0.03420.450675.8295154.111292.8153
40.3906-0.291-0.09510.39560.1360.1378-0.1078-0.68240.03630.01430.0930.08270.5699-0.26350.07450.455-0.02080.01860.6276-0.09820.383463.7314161.8791312.433
52.17170.8669-0.31812.19480.49620.2570.1210.63720.3678-0.6493-0.14780.1195-0.7913-0.53310.23540.54550.2037-0.03610.7204-0.12910.417249.6631175.1336282.2275
61.2295-0.0671-0.2330.41090.83432.82120.0232-0.38960.2973-0.0177-0.15420.0907-0.1821-0.4234-0.02420.39760.0317-0.00160.6532-0.23160.521352.1946177.9261307.8576
71.45690.37430.631.1480.04980.3718-0.03810.1564-0.003-0.0523-0.18220.10510.1323-0.1052-0.0180.37090.0121-0.00390.531-0.08330.432958.4933161.6403284.9664
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 140 )
2X-RAY DIFFRACTION2chain 'A' and (resid 141 through 219 )
3X-RAY DIFFRACTION3chain 'A' and (resid 220 through 296 )
4X-RAY DIFFRACTION4chain 'A' and (resid 297 through 318 )
5X-RAY DIFFRACTION5chain 'B' and (resid 12 through 27 )
6X-RAY DIFFRACTION6chain 'B' and (resid 28 through 282 )
7X-RAY DIFFRACTION7chain 'B' and (resid 283 through 334 )

+
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