[English] 日本語
Yorodumi
- PDB-1bu5: X-RAY CRYSTAL STRUCTURE OF THE DESULFOVIBRIO VULGARIS (HILDENBORO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bu5
TitleX-RAY CRYSTAL STRUCTURE OF THE DESULFOVIBRIO VULGARIS (HILDENBOROUGH) APOFLAVODOXIN-RIBOFLAVIN COMPLEX
ComponentsPROTEIN (FLAVODOXIN)
KeywordsELECTRON TRANSPORT / FLAVOPROTEIN
Function / homology
Function and homology information


FMN binding / electron transfer activity
Similarity search - Function
Flavodoxin, short chain / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin domain / Flavodoxin-like / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Rossmann fold ...Flavodoxin, short chain / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin domain / Flavodoxin-like / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
RIBOFLAVIN / Flavodoxin
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsWalsh, M.A. / Mccarthy, A. / O'Farrell, P.A. / Mccardle, P. / Cunningham, P.D. / Mayhew, S.G. / Higgins, T.M.
Citation
Journal: Eur.J.Biochem. / Year: 1998
Title: X-ray crystal structure of the Desulfovibrio vulgaris (Hildenborough) apoflavodoxin-riboflavin complex.
Authors: Walsh, M.A. / McCarthy, A. / O'Farrell, P.A. / McArdle, P. / Cunningham, P.D. / Mayhew, S.G. / Higgins, T.M.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Comparison of the Crystal Structures of a Flavodoxin in its Three Oxidation States at Cryogenictemperatures
Authors: Watt, W. / Tulinsky, A. / Swenson, R.P. / Watenpaugh, K.D.
#2: Journal: J.Biol.Chem. / Year: 1988
Title: Cloning, Nucleotide Sequence, and Expression of the Flavodoxin Gene from Desulfovibrio Vulgaris (Hildenborough)
Authors: Krey, G.D. / Vanin, E.F. / Swenson, R.P.
#3: Journal: Fems Microbiol.Lett. / Year: 1988
Title: Cloning and Sequencing of the Gene Encoding Flavodoxin from Desulfovibrio Vulgaris Hildenborough
Authors: Curley, G.P. / Voordouw, G.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1973
Title: The Binding of Riboflavin-5-Phosphate in a Flavoprotein. Flavodoxin at 2.0- Angstroms Resolution
Authors: Watenpaugh, K.D. / Sieker, L.C. / Jensen, L.H.
#5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1972
Title: Structure of the Oxidized Form of a Flavodoxin at 2.5-Angstroms Resolution. Resolution of the Phase Ambiguity by Anomalous Scattering
Authors: Watenpaugh, K.D. / Sieker, L.C. / Jensen, L.H. / Legall, J. / Dubourdieu, M.
History
DepositionSep 12, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 9, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PROTEIN (FLAVODOXIN)
B: PROTEIN (FLAVODOXIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3536
Polymers31,4082
Non-polymers9454
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.380, 62.310, 77.420
Angle α, β, γ (deg.)90.00, 127.26, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.38919, -0.92107, 0.01285), (0.92109, -0.38896, 0.01745), (-0.01108, 0.01862, 0.99977)
Vector: 54.31591, -40.74148, -22.5735)

-
Components

#1: Protein PROTEIN (FLAVODOXIN)


Mass: 15704.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P00323
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2 / Riboflavin


Mass: 376.364 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H20N4O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.75 Å3/Da / Density % sol: 55 %
Crystal growpH: 7
Details: CRYSTALS WERE GROWN USING THE HANGING DROP METHOD OF VAPOUR DIFFUSION FROM TRIALS WITH AMMONIUM SULPHATE IN THE CONCENTRATION RANGE 60-80% SATURATION IN 50MM SODIUM PHOSPHATE BUFFER PH 8.0 ...Details: CRYSTALS WERE GROWN USING THE HANGING DROP METHOD OF VAPOUR DIFFUSION FROM TRIALS WITH AMMONIUM SULPHATE IN THE CONCENTRATION RANGE 60-80% SATURATION IN 50MM SODIUM PHOSPHATE BUFFER PH 8.0 CONTAINING 1MM EDTA WITH A PROTEIN CONCENTRATION OF 10-15MG/ML. CRYSTALS APPEAR OVER 1-3 DAYS., pH 7.0
Crystal
*PLUS
Density % sol: 55 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
160-80 %satammonium sulfate1drop
250 mMsodium phosphate1drop
31 mMEDTA1drop
410-15 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.83→20 Å / Num. obs: 26539 / % possible obs: 79.9 % / Observed criterion σ(I): -3 / Redundancy: 1.5 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 15.3
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.5 / % possible all: 83.2
Reflection
*PLUS
Num. measured all: 72050
Reflection shell
*PLUS
% possible obs: 83.2 %

-
Processing

Software
NameClassification
AMoREphasing
CCP4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WILD TYPE FLAVODOXIN COORDINATES NOT DEPOSITED [M.A.WALSH PH.D THESIS NATIONAL UNIVERSITY OF IRELAND (1994)] BUT ESSENTIALLY IDENTICAL TO PDB ENTRY 2FX2

2fx2


Resolution: 1.83→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.202 2037 0.08 %RANDOM
Rwork0.167 ---
obs0.169 26539 81 %-
Displacement parametersBiso mean: 27.1 Å2
Refine analyzeLuzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.83→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2208 0 64 197 2469
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0480.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0480.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.184
X-RAY DIFFRACTIONp_mcangle_it4.45
X-RAY DIFFRACTIONp_scbond_it6.86
X-RAY DIFFRACTIONp_scangle_it10.38
X-RAY DIFFRACTIONp_plane_restr0.0130.02
X-RAY DIFFRACTIONp_chiral_restr0.170.15
X-RAY DIFFRACTIONp_singtor_nbd0.230.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.33
X-RAY DIFFRACTIONp_staggered_tor20.1815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor25.4620
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: CCP4 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 0.08 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_planar_d0.05
X-RAY DIFFRACTIONp_plane_restr0.02
X-RAY DIFFRACTIONp_chiral_restr0.150.17
X-RAY DIFFRACTIONp_mcbond_it43.18
X-RAY DIFFRACTIONp_scbond_it66.8
X-RAY DIFFRACTIONp_mcangle_it54.4
X-RAY DIFFRACTIONp_scangle_it810.3

+
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