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- PDB-1hxd: CRYSTAL STRUCTURE OF E. COLI BIOTIN REPRESSOR WITH BOUND BIOTIN -

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Basic information

Entry
Database: PDB / ID: 1hxd
TitleCRYSTAL STRUCTURE OF E. COLI BIOTIN REPRESSOR WITH BOUND BIOTIN
ComponentsBIRA BIFUNCTIONAL PROTEIN
KeywordsLIGASE / Repressor / BIOTIN / DNA-Binding
Function / homology
Function and homology information


biotin metabolic process / biotin-[biotin carboxyl-carrier protein] ligase / biotin--[biotin carboxyl-carrier protein] ligase activity / biotin biosynthetic process / biotin binding / transcription repressor complex / protein modification process / nucleic acid binding / transcription cis-regulatory region binding / regulation of DNA-templated transcription ...biotin metabolic process / biotin-[biotin carboxyl-carrier protein] ligase / biotin--[biotin carboxyl-carrier protein] ligase activity / biotin biosynthetic process / biotin binding / transcription repressor complex / protein modification process / nucleic acid binding / transcription cis-regulatory region binding / regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / ATP binding / cytoplasm
Similarity search - Function
Biotin operon repressor, helix-turn-helix domain / Bifunctional ligase/repressor BirA / Helix-turn-helix, type 11 / HTH domain / 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 ...Biotin operon repressor, helix-turn-helix domain / Bifunctional ligase/repressor BirA / Helix-turn-helix, type 11 / HTH domain / 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 / 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) / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / SH3 type barrels. / Arc Repressor Mutant, subunit A / Roll / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BIOTIN / Bifunctional ligase/repressor BirA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKwon, K. / Streaker, E.D. / Ruparelia, S. / Beckett, D.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Corepressor-induced organization and assembly of the biotin repressor: a model for allosteric activation of a transcriptional regulator.
Authors: Weaver, L.H. / Kwon, K. / Beckett, D. / Matthews, B.W.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: MULTIPLE DISORDERED LOOPS FUNCTION IN COREPRESOR-INDUCED DIMERIZATION OF THE BIOTIN REPRESSOR
Authors: Kwon, K. / Streaker, E.D. / Ruparelia, S. / Beckett, D.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: E. COLI BIOTIN HOLOENZYME SYNTHETASE/BIO REPRESSOR CRYSTAL STRUCTURE DELINEATES THE BIOTIN- AND DNA-BINDING DOMAINS
Authors: Wilson, K.P. / Shewchuk, L.M. / Brennan, R.G. / Otsuka, A.J. / Matthews, B.W.
History
DepositionJan 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BIRA BIFUNCTIONAL PROTEIN
B: BIRA BIFUNCTIONAL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1924
Polymers70,7042
Non-polymers4892
Water1,06359
1
A: BIRA BIFUNCTIONAL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5962
Polymers35,3521
Non-polymers2441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BIRA BIFUNCTIONAL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5962
Polymers35,3521
Non-polymers2441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.900, 108.900, 143.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein BIRA BIFUNCTIONAL PROTEIN / BIOTIN REPRESSOR


Mass: 35351.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P06709, biotin-[biotin carboxyl-carrier protein] ligase
#2: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.46 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
124 mg/mlprotein1drop
22.3 Msodium potassium phosphate1reservoir

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: UCSD MARK II / Detector: AREA DETECTOR / Date: Sep 2, 1999
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→13 Å / Num. all: 48934 / Num. obs: 26762 / % possible obs: 83 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 9
Reflection shellResolution: 2.4→2.59 Å / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 1.8 / Num. unique all: 4098
Reflection
*PLUS
% possible obs: 83 % / Num. measured all: 48934
Reflection shell
*PLUS
% possible obs: 33 %

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Processing

Software
NameClassification
TNTrefinement
SDMSdata reduction
SDMSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BIA

1bia


Resolution: 2.4→13 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.189 --
all-26762 -
obs-26762 83 %
Refinement stepCycle: LAST / Resolution: 2.4→13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4712 0 32 59 4803
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_angle_deg2.8
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 13 Å / σ(F): 0 / Rfactor all: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 2.8

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