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- PDB-4o1i: Crystal Structure of the regulatory domain of MtbGlnR -

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Basic information

Entry
Database: PDB / ID: 4o1i
TitleCrystal Structure of the regulatory domain of MtbGlnR
ComponentsTranscriptional regulatory protein
KeywordsTRANSCRIPTION REGULATOR / Homodimeric receiver domain
Function / homology
Function and homology information


phosphorelay response regulator activity / nitrate assimilation / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / plasma membrane / cytosol
Similarity search - Function
: / Transcription regulator GlnR, N-terminal domain / OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / CheY-like superfamily / Response regulator ...: / Transcription regulator GlnR, N-terminal domain / OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / CheY-like superfamily / Response regulator / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulatory protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLin, W. / Wang, C. / Zhang, P.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Atypical OmpR/PhoB Subfamily Response Regulator GlnR of Actinomycetes Functions as a Homodimer, Stabilized by the Unphosphorylated Conserved Asp-focused Charge Interactions
Authors: Lin, W. / Wang, Y. / Han, X. / Zhang, Z. / Wang, C. / Wang, J. / Yang, H. / Lu, Y. / Jiang, W. / Zhao, G.P. / Zhang, P.
History
DepositionDec 16, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulatory protein
B: Transcriptional regulatory protein
C: Transcriptional regulatory protein
D: Transcriptional regulatory protein
E: Transcriptional regulatory protein


Theoretical massNumber of molelcules
Total (without water)72,3775
Polymers72,3775
Non-polymers00
Water3,099172
1
A: Transcriptional regulatory protein
B: Transcriptional regulatory protein


Theoretical massNumber of molelcules
Total (without water)28,9512
Polymers28,9512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-5 kcal/mol
Surface area10540 Å2
MethodPISA
2
C: Transcriptional regulatory protein
D: Transcriptional regulatory protein


Theoretical massNumber of molelcules
Total (without water)28,9512
Polymers28,9512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-5 kcal/mol
Surface area10470 Å2
MethodPISA
3
E: Transcriptional regulatory protein

E: Transcriptional regulatory protein


Theoretical massNumber of molelcules
Total (without water)28,9512
Polymers28,9512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y,z1
Buried area1370 Å2
ΔGint-5 kcal/mol
Surface area10480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.241, 144.241, 92.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein
Transcriptional regulatory protein


Mass: 14475.496 Da / Num. of mol.: 5 / Fragment: UNP residues 1-118
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: GlnR, Rv0818 / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O53830
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 3.31 Å3/Da / Density % sol: 62.85 % / Mosaicity: 0.439 °
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7
Details: 1.8M sodium acetate trihydrate, 0.1M Bis-Tris propane, pH 7.0, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 23093 / % possible obs: 99 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.098 / Χ2: 1.328 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.93.10.31922991.142199.7
2.9-3.023.10.2523191.132199.6
3.02-3.153.10.19622831.193199.6
3.15-3.323.10.14923141.246199.3
3.32-3.533.10.11823101.483199
3.53-3.83.10.11323161.455199.3
3.8-4.183.10.10323041.672198.8
4.18-4.793.10.0823061.546198.9
4.79-6.0330.06823011.213198.2
6.03-503.10.05223411.207197.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→38.86 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 1 / SU B: 24.144 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2248 1158 5 %RANDOM
Rwork0.1801 ---
obs0.1824 23076 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 162.2 Å2 / Biso mean: 38.8401 Å2 / Biso min: 13.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å2-0 Å2
2--0.72 Å20 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.8→38.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4111 0 0 172 4283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194177
X-RAY DIFFRACTIONr_angle_refined_deg1.4292.0355715
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3635563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.91323.258132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.70215681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2971537
X-RAY DIFFRACTIONr_chiral_restr0.0820.2743
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213017
X-RAY DIFFRACTIONr_rigid_bond_restr14.74634177
X-RAY DIFFRACTIONr_sphericity_free10.735113
X-RAY DIFFRACTIONr_sphericity_bonded19.90454202
LS refinement shellResolution: 2.802→2.875 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 91 -
Rwork0.276 1616 -
all-1707 -
obs--99.77 %
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)
10.0336-0.0395-0.03380.04650.03950.0354-0.0175-0.0139-0.00770.02210.01310.00880.01780.02280.00440.0559-0.002-0.00910.0675-0.00140.01622.9947-23.827815.3508
20.25940.00140.20930.226-0.27090.49820.0073-0.0483-0.01160.0139-0.018-0.0166-0.0215-0.0210.01070.06310.00230.00070.0566-0.00910.005342.8616-18.97330.1307
30.3116-0.3368-0.140.51240.20580.0831-0.00490.0352-0.0025-0.03260.0067-0.0117-0.01360.0011-0.00190.0630.00340.00080.04510.00750.008638.41334.89556.0731
40.3112-0.14050.10640.1039-0.1170.1581-0.0139-0.006-0.0211-0.01140.0110.00130.033-0.0330.00290.0658-0.0129-0.00940.05360.00080.006352.73410.376236.8499
50.2433-0.0432-0.00940.00830.0020.1492-0.0037-0.03620.0066-0.00590.0063-0.0010.02010.022-0.00260.07490.0012-0.00330.03610.00120.014667.8562-11.894962.0118
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 113
2X-RAY DIFFRACTION2B1 - 113
3X-RAY DIFFRACTION3C1 - 113
4X-RAY DIFFRACTION4D1 - 114
5X-RAY DIFFRACTION5E1 - 113

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