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- PDB-5cj9: Bacillus halodurans Arginine repressor, ArgR -

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Basic information

Entry
Database: PDB / ID: 5cj9
TitleBacillus halodurans Arginine repressor, ArgR
ComponentsArginine repressor
KeywordsTRANSCRIPTION REGULATOR / structural analysis / ArgR / transcriptional regulator
Function / homology
Function and homology information


arginine biosynthetic process / arginine binding / protein complex oligomerization / DNA-binding transcription factor activity / DNA binding / cytoplasm
Similarity search - Function
Arginine repressor / Arginine repressor, C-terminal / Arginine repressor, DNA-binding domain / Arginine repressor, C-terminal domain superfamily / Arginine repressor, DNA binding domain / Arginine repressor, C-terminal domain / Gyrase A; domain 2 - #40 / Gyrase A; domain 2 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...Arginine repressor / Arginine repressor, C-terminal / Arginine repressor, DNA-binding domain / Arginine repressor, C-terminal domain superfamily / Arginine repressor, DNA binding domain / Arginine repressor, C-terminal domain / Gyrase A; domain 2 - #40 / Gyrase A; domain 2 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-1,2-PROPANEDIOL / Arginine repressor
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.409 Å
AuthorsPark, Y.W. / Kang, J. / Yeo, H.Y. / Lee, J.Y.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation2014R1A1A1A05008017 Korea, Republic Of
Agriculture Research Center710003-03-1-SB110 Korea, Republic Of
CitationJournal: Plos One / Year: 2016
Title: Structural Analysis and Insights into the Oligomeric State of an Arginine-Dependent Transcriptional Regulator from Bacillus halodurans.
Authors: Park, Y.W. / Kang, J. / Yeo, H.K. / Lee, J.Y.
History
DepositionJul 14, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arginine repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5192
Polymers16,4431
Non-polymers761
Water1,33374
1
A: Arginine repressor
hetero molecules

A: Arginine repressor
hetero molecules

A: Arginine repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5576
Polymers49,3293
Non-polymers2283
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation12_665-y+1,-z+1,x1
Unit cell
Length a, b, c (Å)104.676, 104.676, 104.676
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-346-

HOH

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Components

#1: Protein Arginine repressor


Mass: 16442.947 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 6-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria)
Strain: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125
Gene: argR, ahrC, BH2777 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K973
#2: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL / Propanediol


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 5%(v/v) 1,2-propanediol, 0.1 M bicine pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 8128 / % possible obs: 100 % / Redundancy: 39.9 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 44.3
Reflection shellResolution: 2.35→2.48 Å / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 12.1 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-20000.1.26data collection
MOSFLM0.1.26data scaling
PHASERphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B4A

1b4a


Resolution: 2.409→27.976 Å / FOM work R set: 0.786 / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2383 349 4.63 %Random
Rwork0.1821 7193 --
obs0.1849 7542 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.15 Å2 / Biso mean: 52.81 Å2 / Biso min: 29.24 Å2
Refinement stepCycle: final / Resolution: 2.409→27.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1150 0 5 74 1229
Biso mean--47.86 57.59 -
Num. residues----146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091169
X-RAY DIFFRACTIONf_angle_d1.241579
X-RAY DIFFRACTIONf_chiral_restr0.045187
X-RAY DIFFRACTIONf_plane_restr0.006204
X-RAY DIFFRACTIONf_dihedral_angle_d14.871447
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4091-3.03460.27371680.207635663734
3.0346-27.97770.2271810.174436273808

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