[English] 日本語
Yorodumi
- PDB-8bvb: Crystal structure of the apo form of SmbA loop deletion mutant. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bvb
TitleCrystal structure of the apo form of SmbA loop deletion mutant.
ComponentsAldo_ket_red domain-containing protein
KeywordsSIGNALING PROTEIN / c-di-GMP receptor / ppGpp / second messenger / TIM barrel
Function / homologyNADP-dependent oxidoreductase domain superfamily / nucleotide binding / metal ion binding / NADP-dependent oxidoreductase domain-containing protein
Function and homology information
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDubey, B.N. / Schirmer, T.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_166652 Switzerland
CitationJournal: Sci Rep / Year: 2023
Title: Mutant structure of metabolic switch protein in complex with monomeric c-di-GMP reveals a potential mechanism of protein-mediated ligand dimerization.
Authors: Dubey, B.N. / Shyp, V. / Fucile, G. / Sondermann, H. / Jenal, U. / Schirmer, T.
History
DepositionDec 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / refine
Item: _pdbx_initial_refinement_model.type / _refine.pdbx_starting_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aldo_ket_red domain-containing protein
B: Aldo_ket_red domain-containing protein
C: Aldo_ket_red domain-containing protein
D: Aldo_ket_red domain-containing protein


Theoretical massNumber of molelcules
Total (without water)128,0844
Polymers128,0844
Non-polymers00
Water22,8791270
1
A: Aldo_ket_red domain-containing protein
B: Aldo_ket_red domain-containing protein

D: Aldo_ket_red domain-containing protein

C: Aldo_ket_red domain-containing protein


Theoretical massNumber of molelcules
Total (without water)128,0844
Polymers128,0844
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
crystal symmetry operation1_655x+1,y,z1
Buried area13890 Å2
ΔGint-51 kcal/mol
Surface area48190 Å2
Unit cell
Length a, b, c (Å)61.375, 208.105, 64.234
Angle α, β, γ (deg.)90.000, 117.575, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein
Aldo_ket_red domain-containing protein


Mass: 32021.057 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Strain: NA 1000 / Gene: CC_2504 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3 / References: UniProt: Q9A5E6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1270 / 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: 2.84 Å3/Da / Density % sol: 56.67 %
Crystal growTemperature: 303 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 200 mM NaCl and 10 % v/w PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97319 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97319 Å / Relative weight: 1
ReflectionResolution: 1.8→56.94 Å / Num. obs: 128620 / % possible obs: 97.84 % / Redundancy: 3.3 % / Biso Wilson estimate: 20.39 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.07474 / Rpim(I) all: 0.04879 / Rrim(I) all: 0.08954 / Net I/σ(I): 12.06
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.5554 / Mean I/σ(I) obs: 2.86 / Num. unique obs: 12871 / CC1/2: 0.763 / CC star: 0.93 / Rpim(I) all: 0.3609 / Rrim(I) all: 0.6642 / % possible all: 97.84

-
Processing

Software
NameVersionClassification
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PHENIX1.19.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GS8

6gs8


Resolution: 1.8→56.94 Å / SU ML: 0.2002 / Cross valid method: FREE R-VALUE / σ(F): 0.94 / Phase error: 21.0485
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2031 6163 4.79 %
Rwork0.1689 122435 -
obs0.1706 128598 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.65 Å2
Refinement stepCycle: LAST / Resolution: 1.8→56.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8952 0 0 1270 10222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00929132
X-RAY DIFFRACTIONf_angle_d1.051312392
X-RAY DIFFRACTIONf_chiral_restr0.0621368
X-RAY DIFFRACTIONf_plane_restr0.011652
X-RAY DIFFRACTIONf_dihedral_angle_d5.37771272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.28312230.24614035X-RAY DIFFRACTION97.89
1.82-1.840.28912340.23734071X-RAY DIFFRACTION98
1.84-1.860.29642180.23664090X-RAY DIFFRACTION97.64
1.86-1.890.26662100.24384034X-RAY DIFFRACTION97.68
1.89-1.910.34972040.254100X-RAY DIFFRACTION97.62
1.91-1.940.29171950.24054039X-RAY DIFFRACTION98.26
1.94-1.970.24382260.21284061X-RAY DIFFRACTION97.77
1.97-20.26561770.19844144X-RAY DIFFRACTION98.43
2-2.030.24261990.18774078X-RAY DIFFRACTION97.96
2.03-2.060.21472090.17854102X-RAY DIFFRACTION98.25
2.06-2.10.23782030.17994064X-RAY DIFFRACTION97.53
2.1-2.130.21452360.18074013X-RAY DIFFRACTION97.9
2.13-2.180.23492440.17574065X-RAY DIFFRACTION98
2.18-2.220.21982130.17984117X-RAY DIFFRACTION98.84
2.22-2.270.21511970.17694105X-RAY DIFFRACTION98.22
2.27-2.320.2331610.18324157X-RAY DIFFRACTION98.47
2.32-2.380.22781810.1864128X-RAY DIFFRACTION98.47
2.38-2.440.2411710.1754131X-RAY DIFFRACTION98.35
2.44-2.510.21351940.16774077X-RAY DIFFRACTION98.18
2.51-2.60.18532210.16784096X-RAY DIFFRACTION97.89
2.6-2.690.21561840.16674110X-RAY DIFFRACTION98.08
2.69-2.80.21461830.16424142X-RAY DIFFRACTION98.36
2.8-2.920.20052130.16054102X-RAY DIFFRACTION98.25
2.92-3.080.19452310.16214048X-RAY DIFFRACTION97.72
3.08-3.270.20251970.16274033X-RAY DIFFRACTION97.2
3.27-3.520.18792360.14883941X-RAY DIFFRACTION95.76
3.52-3.880.16172050.14384046X-RAY DIFFRACTION96.33
3.88-4.440.17171920.13464098X-RAY DIFFRACTION97.63
4.44-5.590.14692290.14334054X-RAY DIFFRACTION97.19
5.59-56.940.16581770.16754154X-RAY DIFFRACTION97.35

+
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://pdbjlvh1.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