[English] 日本語
Yorodumi
- PDB-5wid: Structure of a flavodoxin from the domain Archaea -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wid
TitleStructure of a flavodoxin from the domain Archaea
ComponentsFlavodoxin
KeywordsFLAVOPROTEIN / flavodoxin / Methanosarcina acetivorans
Function / homology
Function and homology information


FMN binding / electron transfer activity
Similarity search - Function
Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily
Similarity search - Domain/homology
ACETATE ION / FLAVIN MONONUCLEOTIDE / Flavodoxin
Similarity search - Component
Biological speciesMethanosarcina acetivorans C2A (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.681 Å
AuthorsMurakami, K.S. / Ferry, J.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM087350 United States
Department of Energy (DOE, United States)DE-FG02-95ER20198 MOD16 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Structure and function of an unusual flavodoxin from the domainArchaea.
Authors: Prakash, D. / Iyer, P.R. / Suharti, S. / Walters, K.A. / Santiago-Martinez, M.G. / Golbeck, J.H. / Murakami, K.S. / Ferry, J.G.
History
DepositionJul 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Oct 4, 2023Group: 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: Flavodoxin
B: Flavodoxin
C: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7579
Polymers49,1523
Non-polymers1,6056
Water8,539474
1
A: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9584
Polymers16,3841
Non-polymers5743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9593
Polymers16,3841
Non-polymers5752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8402
Polymers16,3841
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.773, 112.773, 173.724
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-382-

HOH

21C-352-

HOH

31C-369-

HOH

41C-394-

HOH

51C-407-

HOH

61C-413-

HOH

71C-438-

HOH

81C-453-

HOH

-
Components

#1: Protein Flavodoxin


Mass: 16384.049 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans C2A (archaea)
Strain: ATCC 35395 / DSM 2834 / JCM 12185 / C2A / Gene: MA_1799 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TPV5
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / 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: 3.24 Å3/Da / Density % sol: 62.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris (pH 6.5), 0.2 M ammonium acetate and 20-26 % (w/v) 2-methyl-2,4-pentanediol (MPD)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9181 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9181 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 73408 / % possible obs: 98.1 % / Redundancy: 7.6 % / Net I/σ(I): 30.3

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YCF

1ycf


Resolution: 1.681→27.087 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1733 3704 5.05 %RANDOM
Rwork0.1583 ---
obs0.1591 73343 98.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.681→27.087 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3315 0 109 474 3898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063497
X-RAY DIFFRACTIONf_angle_d0.8884719
X-RAY DIFFRACTIONf_dihedral_angle_d5.0632669
X-RAY DIFFRACTIONf_chiral_restr0.057528
X-RAY DIFFRACTIONf_plane_restr0.005580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.681-1.70310.31521310.28642507X-RAY DIFFRACTION94
1.7031-1.72650.3091190.2582605X-RAY DIFFRACTION96
1.7265-1.75110.24691330.24162564X-RAY DIFFRACTION97
1.7511-1.77720.27781330.22742642X-RAY DIFFRACTION98
1.7772-1.8050.22711320.21362632X-RAY DIFFRACTION98
1.805-1.83460.22361550.20372622X-RAY DIFFRACTION98
1.8346-1.86620.19441500.1832656X-RAY DIFFRACTION99
1.8662-1.90020.2331500.18052620X-RAY DIFFRACTION98
1.9002-1.93670.19341360.17422652X-RAY DIFFRACTION99
1.9367-1.97620.17241430.16792660X-RAY DIFFRACTION99
1.9762-2.01920.1781460.16722659X-RAY DIFFRACTION99
2.0192-2.06610.20611420.16492670X-RAY DIFFRACTION99
2.0661-2.11780.18491530.15542669X-RAY DIFFRACTION99
2.1178-2.1750.15931410.14672686X-RAY DIFFRACTION99
2.175-2.2390.15281520.14872660X-RAY DIFFRACTION99
2.239-2.31120.16731510.14752669X-RAY DIFFRACTION99
2.3112-2.39380.17491660.14952688X-RAY DIFFRACTION100
2.3938-2.48950.18621300.15352711X-RAY DIFFRACTION99
2.4895-2.60280.17011290.15052703X-RAY DIFFRACTION99
2.6028-2.73990.15431340.1472746X-RAY DIFFRACTION100
2.7399-2.91130.15981370.15352729X-RAY DIFFRACTION100
2.9113-3.13580.15111390.15962740X-RAY DIFFRACTION99
3.1358-3.45080.15461550.13852745X-RAY DIFFRACTION99
3.4508-3.94880.14081480.13462756X-RAY DIFFRACTION99
3.9488-4.97010.16141490.13162780X-RAY DIFFRACTION98
4.9701-27.09070.16621500.16842868X-RAY DIFFRACTION95
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)
11.5165-0.3208-0.02430.6705-0.1831.3537-0.0385-0.0847-0.01920.04690.0145-0.02240.0375-0.06390.00370.1369-0.00330.00990.0932-0.01790.101530.001925.2691-1.931
21.5015-1.0223-0.38490.95480.48661.04580.01030.2795-0.3260.0277-0.21090.43690.0836-0.4837-0.17860.149-0.01880.03410.2831-0.08940.21956.202726.7352-7.4966
31.0971-0.9174-0.57811.63071.33551.08810.14880.12210.1627-0.2995-0.1194-0.3097-0.14880.06070.0090.14490.01210.07190.13690.03960.19365.489460.35764.197
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

+
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