[English] 日本語
Yorodumi
- PDB-2vx9: H. salinarum dodecin E45A mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vx9
TitleH. salinarum dodecin E45A mutant
ComponentsDODECIN
KeywordsFLAVOPROTEIN / FLAVIN / ARCHAEA / DODECIN / RIBOFLAVIN / LUMICHROME
Function / homology
Function and homology information


Dodecin / Dodecin-like superfamily / Dodecin / Flavin-binding protein dodecin / Dodecin-like / Dodecin subunit-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RIBOFLAVIN / Dodecin
Similarity search - Component
Biological speciesHALOBACTERIUM SALINARUM R1 (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsGrininger, M. / Staudt, H. / Johansson, P. / Wachtveitl, J. / Oesterhelt, D.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Dodecin is the Key Player in Flavin Homeostasis of Archaea.
Authors: Grininger, M. / Staudt, H. / Johansson, P. / Wachtveitl, J. / Oesterhelt, D.
History
DepositionJul 1, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: DODECIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6869
Polymers7,1121
Non-polymers5758
Water1,27971
1
A: DODECIN
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)92,237108
Polymers85,34112
Non-polymers6,89696
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation34_555-y+1/2,z,-x+1/21
crystal symmetry operation55_555-z+1/2,-x+1/2,y1
crystal symmetry operation11_465y-1/2,-z+1,-x+1/21
crystal symmetry operation8_556-z+1/2,x+1/2,-y+11
crystal symmetry operation77_455z-1/2,x+1/2,y1
crystal symmetry operation52_566x,-y+1,-z+11
crystal symmetry operation26_565-x,-y+1,z1
crystal symmetry operation84_565-y+1/2,-z+1,x+1/21
crystal symmetry operation30_456z-1/2,-x+1/2,-y+11
crystal symmetry operation57_455y-1/2,z,x+1/21
crystal symmetry operation75_556-x,y,-z+11
Buried area30120 Å2
ΔGint-118.84 kcal/mol
Surface area27400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.940, 142.940, 142.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132
Components on special symmetry positions
IDModelComponents
11A-1067-

NA

21A-1068-

CL

31A-1069-

CL

41A-2010-

HOH

51A-2023-

HOH

61A-2071-

HOH

-
Components

#1: Protein DODECIN


Mass: 7111.765 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-65 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HALOBACTERIUM SALINARUM R1 (Halophile) / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM 671) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B0R5M0
#2: Chemical ChemComp-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2


Mass: 376.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N4O6
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 45 TO ALA

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 69 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2 M MGCL2, 2.0 M NACL, 0.1 M NA, HEPES PH 7.5 AND 30% PEG400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 14, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. obs: 15586 / % possible obs: 98 % / Observed criterion σ(I): 3.5 / Redundancy: 10.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.1
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 3.5 / % possible all: 95.8

-
Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CCB

2ccb


Resolution: 1.65→19.1 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.168 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.204 788 5.1 %RANDOM
Rwork0.185 ---
obs0.186 14796 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.13 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms483 0 34 71 588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022517
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4612708
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.083562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.34126.425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4911578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.884152
X-RAY DIFFRACTIONr_chiral_restr0.1380.285
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02388
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.0711.5311
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9812501
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9753206
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.1094.5207
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 64 -
Rwork0.331 1039 -
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