[English] 日本語
Yorodumi
- PDB-1sr8: Structural Genomics, 1.9A crystal structure of cobalamin biosynth... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1sr8
TitleStructural Genomics, 1.9A crystal structure of cobalamin biosynthesis protein (cbiD) from Archaeoglobus fulgidus
Componentscobalamin biosynthesis protein (cbiD)
KeywordsBIOSYNTHETIC PROTEIN / Structural Genomics / Cobalamin biosynthesis protein (cbiD) / Archaeoglobus fulgidus / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


cobalt-precorrin-5B (C1)-methyltransferase / cobalt-precorrin-5B C1-methyltransferase activity / anaerobic cobalamin biosynthetic process / methylation
Similarity search - Function
CbiD-like / CbiD-like / CbiD-like / CbiD-like / CbiD-like domains / Cobalt-precorrin-5B C(1)-methyltransferase CbiD / CbiD superfamily / CbiD / Rossmann fold / 2-Layer Sandwich ...CbiD-like / CbiD-like / CbiD-like / CbiD-like / CbiD-like domains / Cobalt-precorrin-5B C(1)-methyltransferase CbiD / CbiD superfamily / CbiD / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cobalt-precorrin-5B C(1)-methyltransferase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsZhang, R. / Skarina, T. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: 1.9A crystal structure of cobalamin biosynthesis protein (cbiD) from Archaeoglobus fulgidus
Authors: Zhang, R. / Skarina, T. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionMar 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: cobalamin biosynthesis protein (cbiD)


Theoretical massNumber of molelcules
Total (without water)33,2151
Polymers33,2151
Non-polymers00
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.035, 75.912, 63.032
Angle α, β, γ (deg.)90.00, 113.70, 90.00
Int Tables number5
Space group name H-MC121
DetailsThis protein existed as monomer

-
Components

#1: Protein cobalamin biosynthesis protein (cbiD)


Mass: 33215.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O29535
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.61 Å3/Da / Density % sol: 52.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M K/Na Tartr., 20% PEG3350, 0.05M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9795, 0.9797, 0.94656
DetectorType: SBC-3 / Detector: CCD / Date: Feb 18, 2004 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97971
30.946561
ReflectionResolution: 1.9→50 Å / Num. all: 53295 / Num. obs: 52336 / % possible obs: 98.2 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 4 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 24.17
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 2.554 / Num. unique all: 55398 / % possible all: 93

-
Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→26.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 286728.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2189 5 %RANDOM
Rwork0.209 ---
obs0.209 43752 94.8 %-
all-46152 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.1283 Å2 / ksol: 0.393579 e/Å3
Displacement parametersBiso mean: 33.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.65 Å20 Å21.79 Å2
2--3.06 Å20 Å2
3----0.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 1.9→26.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2194 0 0 135 2329
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.7
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.326 93 6.2 %
Rwork0.317 1406 -
obs--16.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

+
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