[English] 日本語
Yorodumi
- PDB-3rux: Crystal structure of biotin-protein ligase BirA from Mycobacteriu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rux
TitleCrystal structure of biotin-protein ligase BirA from Mycobacterium tuberculosis in complex with an acylsulfamide bisubstrate inhibitor
ComponentsBirA bifunctional protein
KeywordsLIGASE/LIGASE INHIBITOR / biotin-protein ligase / LIGASE-LIGASE INHIBITOR complex
Function / homology
Function and homology information


biotin-protein ligase activity / biotin-[biotin carboxyl-carrier protein] ligase / biotin-[acetyl-CoA-carboxylase] ligase activity / small molecule binding / post-translational protein modification
Similarity search - Function
Biotin protein ligase, C-terminal / Biotin protein ligase C terminal domain / Biotin--acetyl-CoA-carboxylase ligase / Biotin/lipoate A/B protein ligase family / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain / SH3 type barrels. - #100 / 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. ...Biotin protein ligase, C-terminal / Biotin protein ligase C terminal domain / Biotin--acetyl-CoA-carboxylase ligase / Biotin/lipoate A/B protein ligase family / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain / SH3 type barrels. - #100 / 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. / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-BS5 / biotin--[biotin carboxyl-carrier protein] ligase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsGeders, T.W. / Finzel, B.C.
CitationJournal: Chem.Biol. / Year: 2011
Title: Bisubstrate Adenylation Inhibitors of Biotin Protein Ligase from Mycobacterium tuberculosis.
Authors: Duckworth, B.P. / Geders, T.W. / Tiwari, D. / Boshoff, H.I. / Sibbald, P.A. / Barry, C.E. / Schnappinger, D. / Finzel, B.C. / Aldrich, C.C.
History
DepositionMay 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BirA bifunctional protein
B: BirA bifunctional protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2124
Polymers57,0692
Non-polymers1,1432
Water11,764653
1
A: BirA bifunctional protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1062
Polymers28,5341
Non-polymers5721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BirA bifunctional protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1062
Polymers28,5341
Non-polymers5721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.882, 68.802, 115.755
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein BirA bifunctional protein / POSSIBLE BIFUNCTIONAL PROTEIN BIRA: BIOTIN OPERON REPRESSOR + BIOTIN--[ACETYL-COA-CARBOXYLASE] ...POSSIBLE BIFUNCTIONAL PROTEIN BIRA: BIOTIN OPERON REPRESSOR + BIOTIN--[ACETYL-COA-CARBOXYLASE] SYNTHETASE (BIOTIN--PROTEIN LIGASE)


Mass: 28534.428 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: birA, MT3379, Rv3279c / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): MACH I
References: UniProt: P96884, biotin-[biotin carboxyl-carrier protein] ligase
#2: Chemical ChemComp-BS5 / 5'-deoxy-5'-[({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}sulfamoyl)amino]adenosine


Mass: 571.630 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29N9O7S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 653 / 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: 2.09 Å3/Da / Density % sol: 41.16 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% MPEG 2000, 50 mM trimethylamine N-oxide, 100 mM Tris, 20% PEG 400 as cryoprotectant, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K, pH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Dec 16, 2009
RadiationMonochromator: Rosenbaum-Rock monochromator Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→43.399 Å / Num. all: 56877 / Num. obs: 55584 / % possible obs: 97.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.8 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.6

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementResolution: 1.7→43.399 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.83 / SU ML: 0.43 / σ(F): 1.34 / Phase error: 23.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2165 2806 5.05 %
Rwork0.1901 52725 -
obs0.1915 55531 97.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.325 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso max: 68.99 Å2 / Biso mean: 23.2336 Å2 / Biso min: 8.43 Å2
Baniso -1Baniso -2Baniso -3
1-2.8322 Å2-0 Å2-0 Å2
2---1.7134 Å20 Å2
3----0.0905 Å2
Refinement stepCycle: LAST / Resolution: 1.7→43.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3880 0 76 653 4609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034164
X-RAY DIFFRACTIONf_angle_d1.0355726
X-RAY DIFFRACTIONf_chiral_restr0.063682
X-RAY DIFFRACTIONf_plane_restr0.004757
X-RAY DIFFRACTIONf_dihedral_angle_d14.5251552
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7001-1.76080.28212090.24534430463983
1.7608-1.83130.27892540.23155067532195
1.8313-1.91470.29222830.245453445627100
1.9147-2.01560.25863000.21653285628100
2.0156-2.14190.23712880.199753405628100
2.1419-2.30730.2452850.20935317560299
2.3073-2.53940.21563080.186653825690100
2.5394-2.90680.22672770.189154155692100
2.9068-3.6620.21263200.177954165736100
3.662-43.41350.16762820.169756865968100

+
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