[English] 日本語
Yorodumi
- PDB-6gnb: Crystal structure of a Ferredoxin-Flavin Thioredoxin Reductase fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gnb
TitleCrystal structure of a Ferredoxin-Flavin Thioredoxin Reductase from Clostridium acetobutylicum at 1.9 A resolution
ComponentsThioredoxin reductase
KeywordsOXIDOREDUCTASE / Flavoprotein / thioredoxin reductase
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
: / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Thioredoxin reductase
Similarity search - Component
Biological speciesClostridium acetobutylicum ATCC 824 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.895 Å
AuthorsBuey, R.M. / Fernandez-Justel, D. / Balsera, M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministry of Economy and CompetitivenessBFU2016-80343-P Spain
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Ferredoxin-linked flavoenzyme defines a family of pyridine nucleotide-independent thioredoxin reductases.
Authors: Buey, R.M. / Fernandez-Justel, D. / de Pereda, J.M. / Revuelta, J.L. / Schurmann, P. / Buchanan, B.B. / Balsera, M.
History
DepositionMay 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2309
Polymers31,7071
Non-polymers1,5228
Water5,134285
1
A: Thioredoxin reductase
hetero molecules

A: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,45918
Polymers63,4152
Non-polymers3,04516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7120 Å2
ΔGint-24 kcal/mol
Surface area26370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.221, 40.942, 81.093
Angle α, β, γ (deg.)90.00, 103.76, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Thioredoxin reductase


Mass: 31707.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum ATCC 824 (bacteria)
Gene: CA_C3082 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97EM8

-
Non-polymers , 5 types, 293 molecules

#2: Chemical ChemComp-FAD / 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-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium thiocyanate, 0.1 M HEPES pH 7.9, 15% (v/v) pentaerythritol propoxylate (5/4 PO/OH)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97923 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.895→42.93 Å / Num. obs: 46948 / % possible obs: 99.59 % / Redundancy: 6.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.1069 / Rrim(I) all: 0.1163 / Net I/σ(I): 10.71
Reflection shellResolution: 1.895→1.963 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.482 / Mean I/σ(I) obs: 1.17 / Num. unique obs: 4604 / CC1/2: 0.504 / Rrim(I) all: 1.607 / % possible all: 98.56

-
Processing

Software
NameVersionClassification
PHENIX(dev_2666: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GNA

6gna


Resolution: 1.895→40.417 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.2 / Phase error: 29.65
RfactorNum. reflection% reflection
Rfree0.2008 6214 4.93 %
Rwork0.1753 --
obs0.1766 46912 97.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.895→40.417 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2149 0 102 285 2536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072333
X-RAY DIFFRACTIONf_angle_d1.013157
X-RAY DIFFRACTIONf_dihedral_angle_d17.128860
X-RAY DIFFRACTIONf_chiral_restr0.074350
X-RAY DIFFRACTIONf_plane_restr0.006395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.295-1.30970.64562030.61153709X-RAY DIFFRACTION90
1.3097-1.32510.4982120.56583943X-RAY DIFFRACTION95
1.3251-1.34130.4972090.52373836X-RAY DIFFRACTION96
1.3413-1.35830.47371990.4893996X-RAY DIFFRACTION96
1.3583-1.37610.43141870.43033936X-RAY DIFFRACTION96
1.3761-1.3950.4392050.43293908X-RAY DIFFRACTION96
1.395-1.41490.40882150.39533945X-RAY DIFFRACTION96
1.4149-1.43610.39272080.3673954X-RAY DIFFRACTION97
1.4361-1.45850.33282030.32913986X-RAY DIFFRACTION96
1.4585-1.48240.31191970.30353960X-RAY DIFFRACTION97
1.4824-1.5080.30242000.30883951X-RAY DIFFRACTION96
1.508-1.53540.3172150.30644024X-RAY DIFFRACTION98
1.5354-1.56490.28382030.2453929X-RAY DIFFRACTION97
1.5649-1.59690.2252370.21854041X-RAY DIFFRACTION98
1.5969-1.63160.2191980.20813939X-RAY DIFFRACTION97
1.6316-1.66950.22432020.19014049X-RAY DIFFRACTION99
1.6695-1.71130.20882220.18894003X-RAY DIFFRACTION97
1.7113-1.75760.18682100.18084000X-RAY DIFFRACTION98
1.7576-1.80930.21612310.17953933X-RAY DIFFRACTION97
1.8093-1.86770.20921940.17793993X-RAY DIFFRACTION97
1.8677-1.93440.19132110.16324106X-RAY DIFFRACTION99
1.9344-2.01190.2092140.1644080X-RAY DIFFRACTION99
2.0119-2.10340.15422010.1583997X-RAY DIFFRACTION99
2.1034-2.21430.18672110.15454080X-RAY DIFFRACTION99
2.2143-2.35310.19392120.15154036X-RAY DIFFRACTION99
2.3531-2.53470.1661940.1484112X-RAY DIFFRACTION99
2.5347-2.78970.18792220.15384044X-RAY DIFFRACTION99
2.7897-3.19330.21382030.16314081X-RAY DIFFRACTION99
3.1933-4.02260.16232160.13674082X-RAY DIFFRACTION99
4.0226-40.43630.16271800.15014119X-RAY DIFFRACTION99
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)
10.62080.32570.75881.6063-0.83163.02020.0463-0.11610.01070.1262-0.0910.0201-0.3096-0.05630.00150.172-0.01510.0230.1799-0.01290.21460.674314.087511.5024
21.2433-0.01061.30651.2268-0.43062.90760.1051-0.1119-0.15810.0879-0.0312-0.10250.0828-0.05470.00530.2283-0.02390.01710.2096-0.00430.24693.50886.162620.3138
31.31760.03790.0920.98980.09090.43330.0226-0.3488-0.22460.0007-0.05260.07470.2447-0.18260.00010.2947-0.01740.02430.37510.04750.27814.34635.302234.9666
42.9215-0.27761.59051.34710.25791.87760.1411-0.2492-0.1436-0.067-0.0668-0.5040.20650.22140.00180.25020.00050.04690.340.06330.343724.19875.456731.9996
50.57970.18870.22271.585-0.66541.62350.1040.021-0.1848-0.05630.0033-0.1620.57130.06430.00030.3229-0.0142-0.03380.19720.00320.26654.1652-2.242611.2675
61.0954-0.5130.03151.68220.22991.5920.03950.0691-0.279-0.090.0650.19210.3944-0.38410.08080.1488-0.0752-0.00770.28080.03160.2329-7.55614.44116.8171
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 132 )
3X-RAY DIFFRACTION3chain 'A' and (resid 133 through 162 )
4X-RAY DIFFRACTION4chain 'A' and (resid 163 through 217 )
5X-RAY DIFFRACTION5chain 'A' and (resid 218 through 262 )
6X-RAY DIFFRACTION6chain 'A' and (resid 263 through 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