[English] 日本語
Yorodumi
- PDB-1l5f: Crystal Structure of CobT complexed with benzimidazole -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1l5f
TitleCrystal Structure of CobT complexed with benzimidazole
ComponentsNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
KeywordsTRANSFERASE / CobT / cobalamin synthetic enzyme / phosphoribosyltransferase / 5 / 6-dimethylbenzimidazole / nicotinate mononucleotide
Function / homology
Function and homology information


nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase / nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity / cobalamin biosynthetic process / nucleotide binding
Similarity search - Function
5,6-Dimethylbenzimidazole Phosphoribosyltransferase; Chain: A; domain 1 / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), small domain / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, bacterial type / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, N-terminal / Phosphoribosyltransferase / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), large domain / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase-like superfamily / Rossmann fold / Orthogonal Bundle ...5,6-Dimethylbenzimidazole Phosphoribosyltransferase; Chain: A; domain 1 / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), small domain / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, bacterial type / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, N-terminal / Phosphoribosyltransferase / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), large domain / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase-like superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BENZIMIDAZOLE / PHOSPHATE ION / Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsCheong, C.-G. / Escalante-Semerena, J. / Rayment, I.
CitationJournal: Biochemistry / Year: 2002
Title: Structural studies of the L-threonine-O-3-phosphate decarboxylase (CobD) enzyme from Salmonella enterica: the apo, substrate, and product-aldimine complexes.
Authors: Cheong, C.G. / Escalante-Semerena, J.C. / Rayment, I.
History
DepositionMar 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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_sheet / 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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9844
Polymers36,6761
Non-polymers3083
Water2,162120
1
A: Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
hetero molecules

A: Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9678
Polymers73,3512
Non-polymers6166
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area5850 Å2
ΔGint-61 kcal/mol
Surface area21200 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.530, 90.000, 47.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212
DetailsThe biological assembly is a dimer generated from one monomer in asymmetric unit by crystallographic two-fold axis

-
Components

#1: Protein Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase / E.C.2.4.2.21 / CobT / NN:DBI PRT / N1-alpha-phosphoribosyltransferase / Nicotinate Mononucleotide:5 / 6- ...CobT / NN:DBI PRT / N1-alpha-phosphoribosyltransferase / Nicotinate Mononucleotide:5 / 6-Dimethylbenzimidazole Phosphoribosyltransferase


Mass: 36675.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: cobt / Plasmid: pT7-5 / Production host: Salmonella enterica (bacteria) / Strain (production host): JE2461
References: UniProt: Q05603, nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-BZI / BENZIMIDAZOLE


Mass: 118.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K

-
Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Details: double focusing mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. all: 23379 / Num. obs: 23379 / % possible obs: 92.2 % / Redundancy: 3 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.3
Reflection shellResolution: 1.9→1.96 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 2.6 / % possible all: 77.2

-
Processing

Software
NameClassification
XDSdata reduction
CNSrefinement
XDSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1D0S

1d0s


Resolution: 1.9→500 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1190 5.1 %random
Rwork0.183 ---
all-23379 --
obs-23379 --
Refinement stepCycle: LAST / Resolution: 1.9→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2423 0 19 120 2562
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.22

+
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