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- PDB-3nhz: Structure of N-terminal Domain of MtrA -

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Basic information

Entry
Database: PDB / ID: 3nhz
TitleStructure of N-terminal Domain of MtrA
ComponentsTwo component system transcriptional regulator mtrA
KeywordsDNA BINDING PROTEIN / Phosphoprotein / Transcription / Transcription regulation / Two-component regulatory system
Function / homology
Function and homology information


biological process involved in interaction with host / phosphorelay response regulator activity / protein-DNA complex / transcription cis-regulatory region binding / protein phosphorylation / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / metal ion binding / plasma membrane / cytosol
Similarity search - Function
: / : / 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 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver 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 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / DNA-binding response regulator MtrA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBarbieri, C.M. / Mack, T.R. / Robinson, V.L. / Miller, M.T. / Stock, A.M.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Regulation of response regulator autophosphorylation through interdomain contacts.
Authors: Barbieri, C.M. / Mack, T.R. / Robinson, V.L. / Miller, M.T. / Stock, A.M.
History
DepositionJun 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2010Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 6, 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Two component system transcriptional regulator mtrA
B: Two component system transcriptional regulator mtrA
C: Two component system transcriptional regulator mtrA
D: Two component system transcriptional regulator mtrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0618
Polymers54,9644
Non-polymers974
Water2,792155
1
A: Two component system transcriptional regulator mtrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7652
Polymers13,7411
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Two component system transcriptional regulator mtrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7652
Polymers13,7411
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Two component system transcriptional regulator mtrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7652
Polymers13,7411
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Two component system transcriptional regulator mtrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7652
Polymers13,7411
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.600, 56.600, 181.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Two component system transcriptional regulator mtrA


Mass: 13741.004 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 1-125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: mtra, TBMG_03294 / Plasmid: PJZG125 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) Gold / References: UniProt: C6DXJ2, UniProt: P9WGM7*PLUS
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 3.06 Å3/Da / Density % sol: 59.79 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 2.6 M NaCl, 100 mM HEPES pH 7.5 and 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 23, 2010 / Details: VARIMAX HR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 25644 / % possible obs: 100 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.102 / Rsym value: 0.066 / Net I/σ(I): 9.1
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.18 / % possible all: 100

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHENIXautomrmodel building
PHENIXrefinerefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXAUTOMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GWR

2gwr


Resolution: 2.5→33.34 Å / Isotropic thermal model: isotropic / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
Rfree0.236 95 -
Rwork0.205 --
all-25596 -
obs-21516 95 %
Displacement parametersBiso mean: 40.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0.32 Å20.49 Å2
2---0.16 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error free: 2.065 Å
Refinement stepCycle: LAST / Resolution: 2.5→33.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3558 0 4 155 3717
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_d1.293
X-RAY DIFFRACTIONf_dihedral_angle_d
X-RAY DIFFRACTIONf_chiral_restr
X-RAY DIFFRACTIONf_plane_restr
LS refinement shellResolution: 2.5→2.589 Å / Total num. of bins used: 1 /
RfactorNum. reflection
Rfree0.3278 166
Rwork0.2623 1878

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