[English] 日本語
Yorodumi
- PDB-3vya: W32Y mutant of FMN-binding protein from Desulfovibrio vulgaris (M... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vya
TitleW32Y mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)
ComponentsFMN-binding protein
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


Pyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / FMN-binding protein
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTakagi, R. / Nakanishi, T. / Kitamura, M.
CitationJournal: To be Published
Title: Crystal structure of W32Y mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)
Authors: Takagi, R. / Nakanishi, T. / Kitamura, M.
History
DepositionSep 22, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5862
Polymers13,1301
Non-polymers4561
Water59433
1
A: FMN-binding protein
hetero molecules

A: FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1734
Polymers26,2602
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area3440 Å2
ΔGint-21 kcal/mol
Surface area11250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.119, 44.119, 178.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein FMN-binding protein


Mass: 13130.030 Da / Num. of mol.: 1 / Mutation: W32Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Strain: Miyazaki F / Gene: DvMF_2023 / Production host: Escherichia coli (E. coli) / References: UniProt: Q46604
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 1.91 Å3/Da / Density % sol: 35.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.05
Details: 100mM HEPES, 85%(v/v) 2-Methyl-2,4-pentanediol, 50%(w/v) polyethylene glycol 400, pH 8.05, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2012
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 4587 / % possible obs: 99.8 % / Redundancy: 15.3 % / Rmerge(I) obs: 0.128
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 15 % / Rmerge(I) obs: 0.258 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FLM

1flm


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.887 / SU B: 8.874 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.747 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27348 209 4.6 %RANDOM
Rwork0.20499 ---
obs0.20811 4323 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.796 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20.2 Å20 Å2
2--0.41 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms908 0 31 33 972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022957
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.991301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6745119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.2722.7540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52815149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.969159
X-RAY DIFFRACTIONr_chiral_restr0.0790.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021725
X-RAY DIFFRACTIONr_mcbond_it0.5751.5591
X-RAY DIFFRACTIONr_mcangle_it1.082946
X-RAY DIFFRACTIONr_scbond_it1.3783366
X-RAY DIFFRACTIONr_scangle_it2.4084.5355
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 20 -
Rwork0.195 306 -
obs--100 %

+
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