[English] 日本語
Yorodumi
- PDB-2ejg: Crystal Structure Of The Biotin Protein Ligase (Mutation R48A) an... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ejg
TitleCrystal Structure Of The Biotin Protein Ligase (Mutation R48A) and Biotin Carboxyl Carrier Protein Complex From Pyrococcus Horikoshii OT3
Components
  • 149aa long hypothetical methylmalonyl-CoA decarboxylase gamma chain
  • 235aa long hypothetical biotin--[acetyl-CoA-carboxylase] ligase
KeywordsLIGASE / Biotinylation / Dimer / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


biotin--[biotin carboxyl-carrier protein] ligase activity / protein modification process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
: / Biotin protein ligase, C-terminal / Biotin protein ligase C terminal domain / Biotin--acetyl-CoA-carboxylase ligase / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile. / Biotin/lipoate A/B protein ligase family / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain / Transcriptional repressor, C-terminal / Biotin-binding site / Biotin-requiring enzymes attachment site. ...: / Biotin protein ligase, C-terminal / Biotin protein ligase C terminal domain / Biotin--acetyl-CoA-carboxylase ligase / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile. / Biotin/lipoate A/B protein ligase family / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain / Transcriptional repressor, C-terminal / Biotin-binding site / Biotin-requiring enzymes attachment site. / SH3 type barrels. - #100 / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE / BIOTIN / 235aa long hypothetical biotin--[acetyl-CoA-carboxylase] ligase / 149aa long hypothetical methylmalonyl-CoA decarboxylase gamma chain
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsBagautdinov, B. / Matsuura, Y. / Bagautdinova, S. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Protein biotinylation visualized by a complex structure of biotin protein ligase with a substrate
Authors: Bagautdinov, B. / Matsuura, Y. / Bagautdinova, S. / Kunishima, N.
History
DepositionMar 16, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 235aa long hypothetical biotin--[acetyl-CoA-carboxylase] ligase
B: 235aa long hypothetical biotin--[acetyl-CoA-carboxylase] ligase
C: 149aa long hypothetical methylmalonyl-CoA decarboxylase gamma chain
D: 149aa long hypothetical methylmalonyl-CoA decarboxylase gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0298
Polymers68,0064
Non-polymers1,0234
Water4,071226
1
A: 235aa long hypothetical biotin--[acetyl-CoA-carboxylase] ligase
C: 149aa long hypothetical methylmalonyl-CoA decarboxylase gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5144
Polymers34,0032
Non-polymers5122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 235aa long hypothetical biotin--[acetyl-CoA-carboxylase] ligase
D: 149aa long hypothetical methylmalonyl-CoA decarboxylase gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5144
Polymers34,0032
Non-polymers5122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.572, 63.487, 74.715
Angle α, β, γ (deg.)90.00, 93.65, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein 235aa long hypothetical biotin--[acetyl-CoA-carboxylase] ligase / BPL


Mass: 26017.408 Da / Num. of mol.: 2 / Mutation: R48A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: bpl / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): (DE3)RIL / References: UniProt: O57883
#2: Protein 149aa long hypothetical methylmalonyl-CoA decarboxylase gamma chain / BCCP


Mass: 7985.457 Da / Num. of mol.: 2 / Fragment: residues 77-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: bccp / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): (DE3)RIL / References: UniProt: O59021
#3: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O3S
#4: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 4.96
Details: 10.5w/v(%) PEG 20000, 0.1M Acet, NaOH, 2.5M Biotin, 2.5M ATP, pH 4.96, microbatch, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 25, 2006 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.71→49.27 Å / Num. obs: 16349 / % possible obs: 91.1 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 55.7 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.093 / Net I/σ(I): 6.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.03 / Num. unique all: 1378 / Rsym value: 0.284 / % possible all: 86.6

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2DZC AND 2D5D

2dzc

2d5d


Resolution: 2.71→38.93 Å / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.273 835 -RANDOM
Rwork0.216 ---
obs0.216 16349 91 %-
all-17941 --
Displacement parametersBiso mean: 43.1 Å2
Baniso -1Baniso -2Baniso -3
1--5.71 Å20 Å23.49 Å2
2---3.92 Å20 Å2
3---9.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.71→38.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4595 0 70 226 4891
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.4021.5
X-RAY DIFFRACTIONc_mcangle_it2.4292
X-RAY DIFFRACTIONc_scbond_it1.9992
X-RAY DIFFRACTIONc_scangle_it3.152.5

+
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