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- PDB-2oqr: The structure of the response regulator RegX3 from Mycobacterium ... -

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Basic information

Entry
Database: PDB / ID: 2oqr
TitleThe structure of the response regulator RegX3 from Mycobacterium tuberculosis
ComponentsSensory transduction protein regX3
KeywordsTRANSCRIPTION / SIGNALING PROTEIN / response regulator / winged-helix-turn-helix / dna-binding / 3D domain swapping / RegX3 / two component system
Function / homology
Function and homology information


regulation of phosphate metabolic process / phosphorelay response regulator activity / phosphorelay signal transduction system / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / DNA binding / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #690 / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Response regulator receiver domain / cheY-homologous receiver domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #690 / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Helix non-globular / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Special / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / BETA-MERCAPTOETHANOL / LANTHANUM (III) ION / Sensory transduction protein RegX3 / Sensory transduction protein RegX3
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.03 Å
AuthorsKing-Scott, J.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The Structure of a Full-length Response Regulator from Mycobacterium tuberculosis in a Stabilized Three-dimensional Domain-swapped, Activated State.
Authors: King-Scott, J. / Nowak, E. / Mylonas, E. / Panjikar, S. / Roessle, M. / Svergun, D.I. / Tucker, P.A.
History
DepositionFeb 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET DETERMINATION METHOD: AUTHOR PROVIDED. THE BIOLOGICAL MOLECULE IS A 3D-DOMAIN SWAPPED DIMER. ...SHEET DETERMINATION METHOD: AUTHOR PROVIDED. THE BIOLOGICAL MOLECULE IS A 3D-DOMAIN SWAPPED DIMER. IN THIS DIMER THE BETA-SHEET A IS IN FACT 5-STRANDED WITH THE FIFTH STRAND COMING FROM THE SECOND MOLECULE. SHEET DETERMINATION METHOD: AUTHOR PROVIDED. THE BETA-SHEET B IS IN FACT AN ANTI-PARALLEL 4-STRANDED BETA-SHEET. IN ORDER TO REPRESENT THIS FEATURE S4 HAS BEEN DEFINED BELOW.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sensory transduction protein regX3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9709
Polymers25,0801
Non-polymers8918
Water2,936163
1
A: Sensory transduction protein regX3
hetero molecules

A: Sensory transduction protein regX3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,94118
Polymers50,1592
Non-polymers1,78116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area8290 Å2
ΔGint-113 kcal/mol
Surface area21140 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)124.351, 124.351, 44.824
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
DetailsThe biological dimer is generated from the monomer in the asymmetric unit by the operation: -x+1/2, y+1/2, -z.

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Components

#1: Protein Sensory transduction protein regX3


Mass: 25079.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Species: Mycobacterium tuberculosis / Strain: H37RV / Gene: regX3 / Plasmid: petM11 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q11156, UniProt: P9WGL9*PLUS
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-LA / LANTHANUM (III) ION


Mass: 138.905 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: La
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 3.45 Å3/Da / Density % sol: 64.38 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Calcium Acetate, 2-4% PEG 4000, 0.1 M Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.813 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 26, 2005
RadiationMonochromator: Si [111], horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.813 Å / Relative weight: 1
ReflectionRedundancy: 16.4 % / Av σ(I) over netI: 6.8 / Number: 314272 / Rmerge(I) obs: 0.136 / Χ2: 0.96 / D res high: 2.7 Å / D res low: 50 Å / Num. obs: 19108 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.325099.310.0640.88415.7
5.817.3210010.0961.0616.4
5.085.8110010.1031.11316.6
4.625.0810010.0941.07116.7
4.294.6210010.091.02416.6
4.034.2910010.11.11116.7
3.834.0310010.121.1616.6
3.663.8310010.1311.11216.7
3.523.6610010.1421.15616.7
3.43.5210010.1661.07616.6
3.33.410010.21.07316.7
3.23.310010.2290.96516.6
3.123.210010.2760.93816.6
3.043.1210010.3250.85516.5
2.973.0410010.3720.82716.4
2.912.9710010.4310.79216.4
2.852.9110010.5280.76316.3
2.82.8510010.5790.73916.2
2.752.810010.6630.72316.1
2.72.7510010.7450.70615.9
ReflectionResolution: 2.03→19.97 Å / Num. all: 23225 / Num. obs: 23179 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 12.1 % / Biso Wilson estimate: 42 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Χ2: 1.404 / Net I/σ(I): 32
Reflection shellResolution: 2.03→2.06 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 4 / Num. unique all: 1112 / Rsym value: 0.664 / Χ2: 1.66 / % possible all: 97.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 2.03→19.97 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.159 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.134 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1188 5.1 %RANDOM
Rwork0.177 ---
all0.179 23225 --
obs0.179 21964 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.019 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.03→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1734 0 17 163 1914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221797
X-RAY DIFFRACTIONr_bond_other_d0.0080.021216
X-RAY DIFFRACTIONr_angle_refined_deg1.5482.0012402
X-RAY DIFFRACTIONr_angle_other_deg1.06932958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.9345227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64923.11777
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.14515316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9261520
X-RAY DIFFRACTIONr_chiral_restr0.090.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021975
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02348
X-RAY DIFFRACTIONr_nbd_refined0.2430.2358
X-RAY DIFFRACTIONr_nbd_other0.1990.21268
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2864
X-RAY DIFFRACTIONr_nbtor_other0.0880.21014
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2127
X-RAY DIFFRACTIONr_metal_ion_refined0.1710.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2990.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2650.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.211
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.3540.23
X-RAY DIFFRACTIONr_mcbond_it11.51175
X-RAY DIFFRACTIONr_mcbond_other0.1741.5461
X-RAY DIFFRACTIONr_mcangle_it1.5572.51820
X-RAY DIFFRACTIONr_scbond_it4.1685678
X-RAY DIFFRACTIONr_scangle_it6.35510581
LS refinement shellResolution: 2.033→2.085 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 86 -
Rwork0.252 1543 -
obs-1629 98.43 %
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)
12.1181.88430.02152.3943-0.43091.54140.1184-0.223-0.2580.187-0.1115-0.27290.13840.0244-0.0069-0.1574-0.0158-0.008-0.15820.0109-0.221430.332-45.4845.228
22.7184-1.38531.72074.4049-0.60387.987-0.0873-0.5366-0.30850.59780.20830.6891-0.2211-0.3437-0.1210.0422-0.04050.1045-0.17710.0996-0.210439.432-13.81117.447
32.4363-0.8496-0.05335.8518-0.60063.6483-0.0648-0.20710.0110.65820.25580.9124-0.2609-0.2897-0.191-0.03860.00660.1205-0.20320.0778-0.087833.689-2.38110.48
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
111 - 1074 - 110
22108 - 171111 - 174
33172 - 226175 - 229

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