[English] 日本語
Yorodumi
- PDB-1obo: W57L flavodoxin from Anabaena -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1obo
TitleW57L flavodoxin from Anabaena
ComponentsFLAVODOXIN
KeywordsELECTRON TRANSFER / FLAVOPROTEIN / ELECTRON TRANSPORT
Function / homology
Function and homology information


cellular response to iron ion starvation / electron transport chain / FMN binding / electron transfer activity
Similarity search - Function
Flavodoxin, long chain / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin domain / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Flavodoxin / Flavodoxin
Similarity search - Component
Biological speciesANABAENA SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsRomero, A. / Ramon, A. / Fernandez-Cabrera, C. / Irun, M.P. / Sancho, J.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: How Fmn Binds to Anabaena Apoflavodoxin: A Hydrophobic Encounter at an Open Binding Site
Authors: Lostao, A. / Daoudi, F. / Irun, M.P. / Ramon, A. / Fernandez-Cabrera, C. / Romero, A. / Sancho, J.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: Closure of a Tyrosine/Tryptophane Aromatic Gate Leeds to a Compact Fold in Apoflavodoxin
Authors: Genzor, C.G. / Perales-Alcon, A. / Sancho, J. / Romero, A.
History
DepositionJan 31, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FLAVODOXIN
B: FLAVODOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5265
Polymers37,5172
Non-polymers1,0093
Water5,567309
1
A: FLAVODOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3113
Polymers18,7581
Non-polymers5522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: FLAVODOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2152
Polymers18,7581
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)37.630, 73.100, 57.050
Angle α, β, γ (deg.)90.00, 102.58, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.86226, 0.50568, 0.02814), (-0.42959, 0.70083, 0.56947), (0.26825, -0.50312, 0.82153)
Vector: -14.04727, -19.60147, -23.5197)

-
Components

#1: Protein FLAVODOXIN /


Mass: 18758.477 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ANABAENA SP. (bacteria) / Strain: PCC 7119 / Cell line: E.COLI JM109 / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TG1 / References: UniProt: P11241, UniProt: P0A3E0*PLUS
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION TRP 57 LEU THE PROTEIN IS A LOW-POTENTIAL ELECTRON DONOR TO A NUMBER OF ENZYMES. ...ENGINEERED MUTATION TRP 57 LEU THE PROTEIN IS A LOW-POTENTIAL ELECTRON DONOR TO A NUMBER OF ENZYMES. MEMBER OF THE FLAVODOXIN FAMILY
Sequence detailsTHE CONFLICT SHOWN IN THE SEQADV RECORDS BELOW ARISE FROM THE CLONING PROCESS AND HAS BEEN ...THE CONFLICT SHOWN IN THE SEQADV RECORDS BELOW ARISE FROM THE CLONING PROCESS AND HAS BEEN DESCRIBED IN M.F. FILLAT, W.E. BORRIAS, P.J. WEISBEEK, BIOCHEM. J. 280, 187-191 (1991)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.03 %
Crystal growpH: 6 / Details: pH 6.00
Crystal grow
*PLUS
Temperature: 295 K / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
23.5 Mammonium sulfate1reservoir
30.1 MMES1reservoirpH6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9102
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 15, 2002 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9102 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. obs: 88832 / % possible obs: 94.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 7.2 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 10.8
Reflection shellResolution: 1.2→1.26 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.138 / Mean I/σ(I) obs: 3.8 / % possible all: 92.1
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 81435 / Num. measured all: 200831 / Rmerge(I) obs: 0.038
Reflection shell
*PLUS
% possible obs: 92.1 % / Num. unique obs: 11496 / Num. measured obs: 28242 / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 3.6

-
Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FLV

1flv


Resolution: 1.2→19.86 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1008568.31 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.202 5364 6 %RANDOM
Rwork0.186 ---
obs0.186 88803 94.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.7723 Å2 / ksol: 0.402019 e/Å3
Displacement parametersBiso mean: 10.5 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å2-0.49 Å2
2--1.59 Å20 Å2
3----0.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.14 Å0.13 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.2→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2650 0 67 309 3026
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.891.5
X-RAY DIFFRACTIONc_mcangle_it1.362
X-RAY DIFFRACTIONc_scbond_it1.612
X-RAY DIFFRACTIONc_scangle_it2.332.5
LS refinement shellResolution: 1.2→1.28 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.215 876 6.1 %
Rwork0.208 13488 -
obs--92 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4PARAM.FMNTOPOLOGY.FMN
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75

+
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