[English] 日本語
Yorodumi
- PDB-3bnk: X-ray crystal structure of Flavoredoxin from Methanosarcina aceti... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bnk
TitleX-ray crystal structure of Flavoredoxin from Methanosarcina acetivorans
ComponentsFlavoredoxin
KeywordsELECTRON TRANSPORT / protein-FMN complex
Function / homology
Function and homology information


: / Flavin reductase like domain / Flavin reductase like domain / Flavin reductase like domain / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Flavoredoxin
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsSuharti, S. / Murakami, K.S. / Ferry, J.G.
CitationJournal: Biochemistry / Year: 2008
Title: Structural and biochemical characterization of flavoredoxin from the archaeon Methanosarcina acetivorans
Authors: Suharti, S. / Murakami, K.S. / de Vries, S. / Ferry, J.G.
History
DepositionDec 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flavoredoxin
B: Flavoredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6394
Polymers43,7262
Non-polymers9132
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.033, 74.828, 75.822
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Flavoredoxin


Mass: 21863.248 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans (archaea) / Strain: C2A / Gene: MA0328 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLacI / References: UniProt: Q8TTU7
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.1 Å3/Da / Density % sol: 41.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris-HCl (pH 8.0), 0.1 M NaBr, 30 % PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5414 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 8, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5414 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 22357 / % possible obs: 98.3 % / Redundancy: 15.2 % / Biso Wilson estimate: 35.2 Å2 / Rmerge(I) obs: 0.095 / Χ2: 1.131 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.05-2.129.50.4418970.90884.9
2.12-2.2112.90.38821820.93498.1
2.21-2.31150.3522370.964100
2.31-2.4315.90.30422330.988100
2.43-2.5816.50.22722541.009100
2.58-2.7816.50.17422581.103100
2.78-3.0616.50.11922691.224100
3.06-3.516.50.07622701.343100
3.5-4.4116.30.04923291.366100
4.41-3015.30.03624281.27199.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å24.01 Å
Translation2.5 Å24.01 Å
Phasing dmFOM : 0.57 / FOM acentric: 0.57 / FOM centric: 0.57 / Reflection: 21897 / Reflection acentric: 19340 / Reflection centric: 2557
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.9-23.9450.850.860.811017741276
3.7-5.90.880.890.7930532554499
2.9-3.70.810.820.7137913308483
2.6-2.90.620.630.5237893380409
2.2-2.60.40.410.3466686051617
2.1-2.20.230.230.2135793306273

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RESOLVE2.12phasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.901 / SU B: 5.457 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.279 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2257 10.1 %RANDOM
Rwork0.208 ---
obs0.214 22285 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.735 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20 Å20 Å2
2--0 Å20 Å2
3----1.41 Å2
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2881 0 62 116 3059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223014
X-RAY DIFFRACTIONr_angle_refined_deg1.3612.0074094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3365371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.25625.652115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.40515512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.288154
X-RAY DIFFRACTIONr_chiral_restr0.0880.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022226
X-RAY DIFFRACTIONr_nbd_refined0.2330.21466
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22018
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2176
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.210
X-RAY DIFFRACTIONr_mcbond_it0.6271.51913
X-RAY DIFFRACTIONr_mcangle_it0.99522990
X-RAY DIFFRACTIONr_scbond_it1.51431352
X-RAY DIFFRACTIONr_scangle_it2.2814.51104
LS refinement shellResolution: 2.05→2.107 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 141 -
Rwork0.272 1249 -
all-1390 -
obs--85.59 %

+
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