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- PDB-3isp: Crystal structure of ArgP from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 3isp
TitleCrystal structure of ArgP from Mycobacterium tuberculosis
ComponentsHTH-type transcriptional regulator Rv1985c/MT2039
KeywordsTRANSCRIPTION / rod shaped structure / DNA binding domain / regulatory domain / DNA-binding / Transcription regulation
Function / homology
Function and homology information


negative regulation of DNA replication / DNA replication origin binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
HTH-type transcriptional regulator ArgP / D-Maltodextrin-Binding Protein; domain 2 - #290 / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / D-Maltodextrin-Binding Protein; domain 2 / Arc Repressor Mutant, subunit A ...HTH-type transcriptional regulator ArgP / D-Maltodextrin-Binding Protein; domain 2 - #290 / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / D-Maltodextrin-Binding Protein; domain 2 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
HTH-type transcriptional regulator LysG / HTH-type transcriptional regulator LysG
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsZhou, X. / Lou, Z. / Sheng, F. / Bartlam, M. / Wang, H. / Rao, Z.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal Structure of ArgP from Mycobacterium tuberculosis Confirms Two Distinct Conformations of Full-length LysR Transcriptional Regulators and Reveals Its Function in DNA Binding and Transcriptional Regulation.
Authors: Zhou, X. / Lou, Z. / Fu, S. / Yang, A. / Shen, H. / Li, Z. / Feng, Y. / Bartlam, M. / Wang, H. / Rao, Z.
History
DepositionAug 27, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 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: HTH-type transcriptional regulator Rv1985c/MT2039
B: HTH-type transcriptional regulator Rv1985c/MT2039


Theoretical massNumber of molelcules
Total (without water)65,7572
Polymers65,7572
Non-polymers00
Water1,38777
1
A: HTH-type transcriptional regulator Rv1985c/MT2039
B: HTH-type transcriptional regulator Rv1985c/MT2039

A: HTH-type transcriptional regulator Rv1985c/MT2039
B: HTH-type transcriptional regulator Rv1985c/MT2039


Theoretical massNumber of molelcules
Total (without water)131,5154
Polymers131,5154
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_566x,-y+1,-z+3/21
Buried area10670 Å2
ΔGint-69 kcal/mol
Surface area50220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.800, 116.740, 136.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein HTH-type transcriptional regulator Rv1985c/MT2039


Mass: 32878.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37V / Gene: Rv1985c / Plasmid: pET-29b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P67665, UniProt: P9WMF5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.6 Å3/Da / Density % sol: 52.74 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 1.6M Na2HPO4/NaH2PO4, pH5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 62.54 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 25.8
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.602 / Mean I/σ(I) obs: 2.6 / % possible all: 93

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→48.606 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.773 / SU ML: 2.21 / σ(F): 0.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.271 2621 7.52 %
Rwork0.207 --
obs0.212 34831 95.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.689 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso max: 132.68 Å2 / Biso mean: 71.169 Å2 / Biso min: 31.72 Å2
Baniso -1Baniso -2Baniso -3
1-3.093 Å20 Å2-0 Å2
2--7.859 Å2-0 Å2
3----10.952 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4190 0 0 77 4267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074273
X-RAY DIFFRACTIONf_angle_d1.115811
X-RAY DIFFRACTIONf_chiral_restr0.07674
X-RAY DIFFRACTIONf_plane_restr0.005755
X-RAY DIFFRACTIONf_dihedral_angle_d17.3881541
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.7490.3551200.3031477159784
2.749-2.8020.4061240.3061525164986
2.802-2.8590.3461360.2991588172488
2.859-2.9210.3121300.2861593172390
2.921-2.9890.4171370.2621640177794
2.989-3.0640.271410.2511673181494
3.064-3.1470.3251350.2211705184095
3.147-3.2390.3431350.2171688182397
3.239-3.3440.3061400.2191712185296
3.344-3.4640.3081350.2011737187298
3.464-3.6020.2681440.1991754189899
3.602-3.7660.2391460.1971750189699
3.766-3.9640.3231360.1781774191099
3.964-4.2130.2251430.18517591902100
4.213-4.5380.2391440.1651785192999
4.538-4.9940.2161410.16717761917100
4.994-5.7160.2331420.19417561898100
5.716-7.1970.2491430.20117791922100
7.197-48.6140.2311490.21739188898

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