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- PDB-5jvo: Crystal structure of the Arginine Repressor from the pathogenic b... -

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Basic information

Entry
Database: PDB / ID: 5jvo
TitleCrystal structure of the Arginine Repressor from the pathogenic bacterium Corynebacterium pseudotuberculosis
ComponentsArginine repressor
KeywordsDNA BINDING PROTEIN / Arginine repressor
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 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
TYROSINE / Arginine repressor / Arginine repressor
Similarity search - Component
Biological speciesCorynebacterium pseudotuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMariutti, R.B. / Ullah, A. / Murakami, M.T. / Arni, R.K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: Tyrosine binding and promiscuity in the arginine repressor from the pathogenic bacterium Corynebacterium pseudotuberculosis.
Authors: Mariutti, R.B. / Ullah, A. / Araujo, G.C. / Murakami, M.T. / Arni, R.K.
History
DepositionMay 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,7265
Polymers21,2682
Non-polymers4583
Water82946
1
A: Arginine repressor
B: Arginine repressor
hetero molecules

A: Arginine repressor
B: Arginine repressor
hetero molecules

A: Arginine repressor
B: Arginine repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,17915
Polymers63,8036
Non-polymers1,3759
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
Buried area9570 Å2
ΔGint-82 kcal/mol
Surface area18420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.191, 83.191, 83.191
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-319-

HOH

21B-313-

HOH

31B-315-

HOH

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Components

#1: Protein Arginine repressor


Mass: 10633.909 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium pseudotuberculosis (bacteria)
Gene: argR, CpE19_0967 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E3UAP8, UniProt: D9QA55*PLUS
#2: Chemical ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM Tris-HCl 200 mM NaCl 10% ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 1.9→48 Å / Num. obs: 15299 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Biso Wilson estimate: 36.141 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Net I/σ(I): 20.81
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.9-2.020.8992.15199.5
2.02-2.160.474.481100
2.16-2.330.3257.271100
2.33-2.550.22811.441100
2.55-2.850.13219.031100
2.85-3.290.07831.131100
3.29-4.030.04551.461100
4.03-5.680.03764.371100
5.68-48.030.03265.66199.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ERE

3ere


Resolution: 1.9→48 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.119 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.127 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2249 764 5 %RANDOM
Rwork0.1797 ---
obs0.1819 14533 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 93.78 Å2 / Biso mean: 34.866 Å2 / Biso min: 19.52 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.9→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1158 0 31 46 1235
Biso mean--33.3 38.24 -
Num. residues----153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0191204
X-RAY DIFFRACTIONr_bond_other_d0.0020.021179
X-RAY DIFFRACTIONr_angle_refined_deg2.3721.9931623
X-RAY DIFFRACTIONr_angle_other_deg1.15732706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7935151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.33923.20853
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.71415205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6641512
X-RAY DIFFRACTIONr_chiral_restr0.1450.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211337
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02259
X-RAY DIFFRACTIONr_mcbond_it2.4142.67616
X-RAY DIFFRACTIONr_mcbond_other2.4152.671615
X-RAY DIFFRACTIONr_mcangle_it3.3473.978763
LS refinement shellResolution: 1.904→1.953 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 50 -
Rwork0.268 1048 -
all-1098 -
obs--99.73 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.77240.12960.43740.09110.24870.7077-0.0135-0.06940.0704-0.00690-0.0023-0.04290.0040.01350.034-0.0146-0.01570.0367-0.01560.025441.398512.32389.7505
21.7122-0.72270.19191.0244-0.50140.32-0.0753-0.07090.08980.18930.0638-0.0669-0.1103-0.07250.01150.0560.01680.00110.04120.00180.016522.397925.045975.7758
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A82 - 160
2X-RAY DIFFRACTION2B86 - 159

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