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- PDB-2p5m: C-terminal domain hexamer of AhrC bound with L-arginine -

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Basic information

Entry
Database: PDB / ID: 2p5m
TitleC-terminal domain hexamer of AhrC bound with L-arginine
ComponentsArginine repressor
KeywordsDNA BINDING PROTEIN / alpha-beta / L-arginine binding domain
Function / homology
Function and homology information


arginine catabolic process to ornithine / 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 DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...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 DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ARGININE / Arginine repressor
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGarnett, J.A. / Baumberg, S. / Stockley, P.G. / Phillips, S.E.V.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Structure of the C-terminal effector-binding domain of AhrC bound to its corepressor L-arginine.
Authors: Garnett, J.A. / Baumberg, S. / Stockley, P.G. / Phillips, S.E.
History
DepositionMar 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 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 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arginine repressor
B: Arginine repressor
C: Arginine repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7468
Polymers27,8703
Non-polymers8765
Water3,045169
1
A: Arginine repressor
B: Arginine repressor
C: Arginine repressor
hetero molecules

A: Arginine repressor
B: Arginine repressor
C: Arginine repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,49216
Polymers55,7406
Non-polymers1,75210
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Unit cell
Length a, b, c (Å)117.014, 117.014, 68.927
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-183-

HOH

21B-244-

HOH

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Components

#1: Protein Arginine repressor / Arginine hydroxamate resistance protein


Mass: 9289.932 Da / Num. of mol.: 3 / Fragment: C-terminal domain (residues 67-149) / Mutation: D67M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: argR, ahrC / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P17893
#2: Chemical
ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.44 Å3/Da / Density % sol: 49.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 28% PEG 400, 0.1M Tris-HCl, 0.2M magnesium chloride, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 23, 2003 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→24.11 Å / Num. obs: 20787 / % possible obs: 99.9 % / Redundancy: 16.7 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 32.4
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 6.6 / Num. unique all: 36574 / Rsym value: 0.391 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1B4B, Trimer of C-terminal domains from B. steareothermophilus

1b4b


Resolution: 1.95→24.11 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.085 / SU ML: 0.097
Isotropic thermal model: Individual isotropic temperature factors and individual TLS parameters for chains A-C
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2057 10.2 %RANDOM
Rwork0.182 ---
obs0.187 20217 97.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.466 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20.23 Å20 Å2
2--0.46 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.95→24.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1843 0 44 174 2061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221901
X-RAY DIFFRACTIONr_angle_refined_deg1.4152.0062556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1515237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81825.275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.47215378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.021513
X-RAY DIFFRACTIONr_chiral_restr0.0940.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021365
X-RAY DIFFRACTIONr_nbd_refined0.2250.21117
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21338
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.238
X-RAY DIFFRACTIONr_mcbond_it0.8941.51235
X-RAY DIFFRACTIONr_mcangle_it1.16521947
X-RAY DIFFRACTIONr_scbond_it2.2513718
X-RAY DIFFRACTIONr_scangle_it3.7054.5609
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 120 -
Rwork0.194 1260 -
obs-1380 93.05 %

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