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- PDB-1i5d: STRUCTURE OF CHEA DOMAIN P4 IN COMPLEX WITH TNP-ATP -

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Basic information

Entry
Database: PDB / ID: 1i5d
TitleSTRUCTURE OF CHEA DOMAIN P4 IN COMPLEX WITH TNP-ATP
ComponentsCHEMOTAXIS PROTEIN CHEA
KeywordsSIGNALING PROTEIN / TRANSFERASE / beta-alpha sandwich
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / chemotaxis / protein domain specific binding / ATP binding / cytoplasm
Similarity search - Function
Chemotaxis protein CheA, P2 response regulator-binding / Chemotaxis protein CheA, P2 response regulator-binding domain superfamily / P2 response regulator binding domain / Histidine kinase CheA-like, homodimeric domain / CheY-binding domain of CheA / Histidine kinase CheA-like, homodimeric domain superfamily / Signal transducing histidine kinase, homodimeric domain / Signal transducing histidine kinase, homodimeric domain / : / CheW-like domain profile. ...Chemotaxis protein CheA, P2 response regulator-binding / Chemotaxis protein CheA, P2 response regulator-binding domain superfamily / P2 response regulator binding domain / Histidine kinase CheA-like, homodimeric domain / CheY-binding domain of CheA / Histidine kinase CheA-like, homodimeric domain superfamily / Signal transducing histidine kinase, homodimeric domain / Signal transducing histidine kinase, homodimeric domain / : / CheW-like domain profile. / CheW-like domain / CheW-like domain superfamily / CheW-like domain / Two component signalling adaptor domain / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-128 / Chemotaxis protein CheA
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBilwes, A.M. / Quezada, C.M. / Croal, L.R. / Crane, B.R. / Simon, M.I.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Nucleotide binding by the histidine kinase CheA.
Authors: Bilwes, A.M. / Quezada, C.M. / Croal, L.R. / Crane, B.R. / Simon, M.I.
History
DepositionFeb 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 23, 2015Group: Non-polymer description
Revision 1.4Aug 9, 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_validate_chiral / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: CHEMOTAXIS PROTEIN CHEA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3374
Polymers21,4271
Non-polymers9103
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.190, 85.190, 73.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Cell settingtetragonal
Space group name H-MP4322

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Components

#1: Protein CHEMOTAXIS PROTEIN CHEA / E.C.2.7.3.- / CHEMOTAXIS SENSOR HISTIDINE KINASE CHEA / CHEA


Mass: 21426.852 Da / Num. of mol.: 1 / Fragment: DOMAIN P4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q56310, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-128 / SPIRO(2,4,6-TRINITROBENZENE[1,2A]-2O',3O'-METHYLENE-ADENINE-TRIPHOSPHATE


Type: RNA linking / Mass: 718.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17N8O19P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.12 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: sodium acetate 0.1 M Ammonium sulfate 1.9 M, pH 4.7. VAPOR DIFFUSION, HANGING DROP at 298 K
Crystal grow
*PLUS
Temperature: 25 ℃ / PH range low: 4.9 / PH range high: 4.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150-80 mg/mlprotein1drop
210 mMnucleotide1drop
310 mM1dropMgCl2
41.8-2.0 Mammonium sulfate1reservoir
50.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 17, 1999
RadiationMonochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 7933 / Num. obs: 7933 / % possible obs: 99 % / Observed criterion σ(I): 1 / Redundancy: 1 % / Biso Wilson estimate: 85.6 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 30
Reflection shellResolution: 2.9→3.04 Å / Redundancy: 1 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 8 / % possible all: 99
Reflection
*PLUS
% possible obs: 99 %
Reflection shell
*PLUS
% possible obs: 99 % / Mean I/σ(I) obs: 8

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B3Q

1b3q


Resolution: 2.9→27.89 Å / Rfactor Rfree error: 0.018 / Data cutoff high absF: 92361613.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.312 316 5.4 %RANDOM
Rwork0.263 ---
all0.263 7933 --
obs0.263 5811 90.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 103.9 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso mean: 89.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20 Å20 Å2
2--1.19 Å20 Å2
3----2.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.5 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.75 Å
Refinement stepCycle: LAST / Resolution: 2.9→27.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1455 0 56 47 1558
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d1.29
X-RAY DIFFRACTIONc_mcbond_it5.891.5
X-RAY DIFFRACTIONc_mcangle_it9.792
X-RAY DIFFRACTIONc_scbond_it8.072
X-RAY DIFFRACTIONc_scangle_it12.122.5
LS refinement shellResolution: 2.9→3 Å / Rfactor Rfree error: 0.097 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.435 20 4.2 %
Rwork0.419 452 -
obs--74.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.TOP
X-RAY DIFFRACTION3TNP2.PARAMTNP2.TOP
X-RAY DIFFRACTION4WATER.PARAM
X-RAY DIFFRACTION5ION.PARAM
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 5.4 % / Rfactor obs: 0.25 / Rfactor Rfree: 0.308
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 89.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.29
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.365 / % reflection Rfree: 4.2 % / Rfactor Rwork: 0.394

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