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- PDB-6azr: Crystal structure of the T264A HK853cp-BeF3-RR468 complex -

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Basic information

Entry
Database: PDB / ID: 6azr
TitleCrystal structure of the T264A HK853cp-BeF3-RR468 complex
Components
  • Chemotaxis regulator-transmits chemoreceptor signals to flagelllar motor components CheY
  • Sensor histidine kinase
KeywordsSIGNALING PROTEIN / Kinase / Phosphatase / Response Regulator / Two-Component System
Function / homology
Function and homology information


histidine phosphotransfer kinase activity / phosphorelay response regulator activity / phosphorelay sensor kinase activity / histidine kinase / phosphorelay signal transduction system / DNA binding / ATP binding / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / : / Histidine kinase/HSP90-like ATPase / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. ...Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / : / Histidine kinase/HSP90-like ATPase / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / Histidine kinase-like ATPase, C-terminal domain / cheY-homologous receiver domain / Heat Shock Protein 90 / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Response regulator / histidine kinase / Chemotaxis regulator-transmits chemoreceptor signals to flagelllar motor components CheY
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.628 Å
AuthorsRose, J. / Zhou, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115355 United States
CitationJournal: Nat Commun / Year: 2017
Title: A pH-gated conformational switch regulates the phosphatase activity of bifunctional HisKA-family histidine kinases.
Authors: Liu, Y. / Rose, J. / Huang, S. / Hu, Y. / Wu, Q. / Wang, D. / Li, C. / Liu, M. / Zhou, P. / Jiang, L.
History
DepositionSep 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sensor histidine kinase
B: Chemotaxis regulator-transmits chemoreceptor signals to flagelllar motor components CheY
C: Sensor histidine kinase
D: Chemotaxis regulator-transmits chemoreceptor signals to flagelllar motor components CheY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,1098
Polymers87,0484
Non-polymers1,0614
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9280 Å2
ΔGint-77 kcal/mol
Surface area31180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.458, 98.336, 71.458
Angle α, β, γ (deg.)90.00, 109.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Sensor histidine kinase


Mass: 29479.449 Da / Num. of mol.: 2 / Fragment: UNP residues 232-489 / Mutation: T264A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0853 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZV7
#2: Protein Chemotaxis regulator-transmits chemoreceptor signals to flagelllar motor components CheY


Mass: 14044.450 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: Tmari_0465 / Production host: Escherichia coli (E. coli) / References: UniProt: R4NNQ5, UniProt: Q9WYT9*PLUS
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
Has protein modificationY

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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: 3.66 Å3/Da / Density % sol: 66.42 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.05 M citric acid , 0.104 M ammonium sulfate, 2 mM AMPPNP, 5 mM Tris, 3.5 mM MgCl2, 2.5 mM BeCl2, 15 mM NaF

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.628→45.5 Å / Num. obs: 13230 / % possible obs: 100 % / Redundancy: 4.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.1444 / Rrim(I) all: 0.1647 / Net I/σ(I): 6.56
Reflection shellResolution: 3.628→3.758 Å / Redundancy: 4 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 2.41 / Num. unique all: 1272 / CC1/2: 0.767 / Rrim(I) all: 0.6143 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DGE

3dge


Resolution: 3.628→45.497 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2396 662 5.01 %
Rwork0.208 --
obs0.2095 13217 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.628→45.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5398 0 64 0 5462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025562
X-RAY DIFFRACTIONf_angle_d0.5467553
X-RAY DIFFRACTIONf_dihedral_angle_d10.1493337
X-RAY DIFFRACTIONf_chiral_restr0.04897
X-RAY DIFFRACTIONf_plane_restr0.003952
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6285-3.90850.29421320.26542468X-RAY DIFFRACTION99
3.9085-4.30160.26921330.22842476X-RAY DIFFRACTION100
4.3016-4.92340.22471280.19222512X-RAY DIFFRACTION100
4.9234-6.20040.27911370.23122529X-RAY DIFFRACTION100
6.2004-45.50030.19951320.17982570X-RAY DIFFRACTION100

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