[English] 日本語
Yorodumi
- PDB-9rxf: E20K/N28G/V36L/D43K/Q48E/I59A/E61K/E72K/V76L/N79S/I92A/D126K/A142... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9rxf
TitleE20K/N28G/V36L/D43K/Q48E/I59A/E61K/E72K/V76L/N79S/I92A/D126K/A142V/D153K/D154E/S158T FLAVODOXIN FROM ANABAENA
ComponentsFlavodoxin
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


electron transport chain / FMN binding / electron transfer activity
Similarity search - Function
Flavodoxin, long chain / : / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Flavodoxin
Similarity search - Component
Biological speciesNostoc sp. PCC 7119 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMartinez-Julvez, M. / Perez-Correa, V. / Sancho, J. / Hidalgo-Toledo, A.
Funding support Spain, 2items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2022-141068NB-I00 Spain
Other governmentE35_23R
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Protein thermostabilization with Protposer: Pushing the stability limits and folding reversibility of a highly-stabilized apoflavodoxin.
Authors: Hidalgo-Toledo, A. / Bazco, D. / Correa-Perez, V. / Martinez-Julvez, M. / Sancho, J.
History
DepositionJul 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flavodoxin
B: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6195
Polymers37,6142
Non-polymers1,0053
Water4,179232
1
A: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2632
Polymers18,8071
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3553
Polymers18,8071
Non-polymers5482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.516, 64.972, 81.127
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Flavodoxin


Mass: 18806.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. PCC 7119 (bacteria) / Gene: isiB / Production host: Escherichia coli (E. coli) / References: UniProt: P0A3E0
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 28% PEG 4000, 0.1 M Tris-HCl, pH 8.5 and 0.2 M MgCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Feb 27, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.4→81.13 Å / Num. obs: 60145 / % possible obs: 99.4 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.028 / Rrim(I) all: 0.076 / Net I/σ(I): 13.3
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.876 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 8583 / Rpim(I) all: 0.339 / Rrim(I) all: 0.941 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
SCALA3.3.22data scaling
MOLREP11.9.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→46.96 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.25 / SU ML: 0.049 / Cross valid method: FREE R-VALUE / ESU R: 0.066 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20612 3086 5.1 %RANDOM
Rwork0.18006 ---
obs0.18139 56989 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.943 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å2-0 Å2-0 Å2
2---0.64 Å2-0 Å2
3---1.29 Å2
Refinement stepCycle: 1 / Resolution: 1.4→46.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2646 0 68 232 2946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122767
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162552
X-RAY DIFFRACTIONr_angle_refined_deg1.8171.8083739
X-RAY DIFFRACTIONr_angle_other_deg0.6571.7845890
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4715334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.05958
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38710476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1170.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023242
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02630
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9051.8041342
X-RAY DIFFRACTIONr_mcbond_other1.9031.8041342
X-RAY DIFFRACTIONr_mcangle_it2.7773.2321674
X-RAY DIFFRACTIONr_mcangle_other2.7793.2331675
X-RAY DIFFRACTIONr_scbond_it3.1872.0841425
X-RAY DIFFRACTIONr_scbond_other3.1862.0861426
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.853.6672066
X-RAY DIFFRACTIONr_long_range_B_refined5.59320.393275
X-RAY DIFFRACTIONr_long_range_B_other5.52719.413228
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 227 -
Rwork0.271 4100 -
obs--98.16 %

+
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