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- PDB-1f9n: CRYSTAL STRUCTURE OF AHRC, THE ARGININE REPRESSOR/ACTIVATOR PROTE... -

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Basic information

Entry
Database: PDB / ID: 1f9n
TitleCRYSTAL STRUCTURE OF AHRC, THE ARGININE REPRESSOR/ACTIVATOR PROTEIN FROM BACILLUS SUBTILIS
ComponentsARGININE REPRESSOR/ACTIVATOR PROTEIN
KeywordsDNA BINDING PROTEIN / WINGED-HELIX-TURN-HELIX / ARGININE REPRESSOR
Function / homology
Function and homology information


regulation of arginine biosynthetic process / : / : / L-arginine biosynthetic process / arginine binding / protein complex oligomerization / cis-regulatory region sequence-specific DNA binding / transcription regulator complex / DNA-binding transcription factor activity / 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
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsDennis, C.A. / Glykos, N.M. / Parsons, M.R. / Phillips, S.E.V.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: The structure of AhrC, the arginine repressor/activator protein from Bacillus subtilis.
Authors: Dennis C, C.A. / Glykos, N.M. / Parsons, M.R. / Phillips, S.E.
History
DepositionJul 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ARGININE REPRESSOR/ACTIVATOR PROTEIN
B: ARGININE REPRESSOR/ACTIVATOR PROTEIN
C: ARGININE REPRESSOR/ACTIVATOR PROTEIN
D: ARGININE REPRESSOR/ACTIVATOR PROTEIN
E: ARGININE REPRESSOR/ACTIVATOR PROTEIN
F: ARGININE REPRESSOR/ACTIVATOR PROTEIN


Theoretical massNumber of molelcules
Total (without water)101,1276
Polymers101,1276
Non-polymers00
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11450 Å2
ΔGint-74 kcal/mol
Surface area42430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)230.310, 73.860, 138.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a hexamer with 32 symmetry. The hexamer is formed by a dimer of trimers.

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Components

#1: Protein
ARGININE REPRESSOR/ACTIVATOR PROTEIN / AHRC


Mass: 16854.479 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: UniProt: P17893
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.92 Å3/Da / Density % sol: 57.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: PEG 4000, ammonium sulphate, phosphate buffer, protease inhibitors (PMSF, TPCK) in isopropanol, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
260 mMammonium sulfate1reservoir
3100 mMphosphate1reservoirpH4.9
43 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 4, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 44888 / Num. obs: 28055 / % possible obs: 88.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 1.6 % / Biso Wilson estimate: 66.8 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 10
Reflection shellResolution: 2.7→2.87 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.14 / Num. unique all: 4440 / % possible all: 85.7

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementResolution: 2.7→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1409 -random
Rwork0.22 ---
all0.22 44888 --
obs0.22 28055 88.7 %-
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6869 0 0 240 7109
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 30 Å / σ(F): 0 / Rfactor obs: 0.22 / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1
LS refinement shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.87 Å / Rfactor Rfree: 0.33 / Rfactor Rwork: 0.27 / Num. reflection Rwork: 4440

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