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- PDB-1i58: STRUCTURE OF THE HISTIDINE KINASE CHEA ATP-BINDING DOMAIN IN COMP... -

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Basic information

Entry
Database: PDB / ID: 1i58
TitleSTRUCTURE OF THE HISTIDINE KINASE CHEA ATP-BINDING DOMAIN IN COMPLEX WITH ATP ANALOG ADPCP AND MAGNESIUM
ComponentsCHEMOTAXIS PROTEIN CHEA
KeywordsSIGNALING PROTEIN / TRANSFERASE / beta-alpha sandwich
Function / homology
Function and homology information


phosphorelay sensor kinase activity / histidine kinase / 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 superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / Chemotaxis protein CheA
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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.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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHEMOTAXIS PROTEIN CHEA
B: CHEMOTAXIS PROTEIN CHEA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2337
Polymers42,1592
Non-polymers1,0755
Water4,468248
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.820, 48.930, 77.040
Angle α, β, γ (deg.)90.00, 103.54, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 21079.270 Da / Num. of mol.: 2 / Fragment: DOMAIN P4 / Mutation: R354H, I353S, K352G
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

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Non-polymers , 5 types, 253 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 8000 33-36% Ammonium acetate 0.8 M sodium acetate 0.085 M pH 4.5. VAPOR DIFFUSION, HANGING DROP at 293 K
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 4.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150-80 mg/mlprotein1drop
210 mMnucleotide1drop
310 mM1dropMgCl2
433-36 %(w/v)PEG80001reservoir
50.8 Mammonium acetate1reservoir
60.085 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.03 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 8, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 38000 / Num. obs: 38000 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 22
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 3 / % possible all: 97
Reflection
*PLUS
% possible obs: 98 %
Reflection shell
*PLUS
% possible obs: 97 % / Mean I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
EPMRphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1B3Q

1b3q


Resolution: 1.6→19.84 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 30531988.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3694 10 %RANDOM
Rwork0.223 ---
all0.223 38000 --
obs0.223 36763 93.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.43 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso mean: 23.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.9 Å20 Å24.36 Å2
2---2.71 Å20 Å2
3---6.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.6→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2845 0 67 248 3160
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it0.641.5
X-RAY DIFFRACTIONc_mcangle_it1.132
X-RAY DIFFRACTIONc_scbond_it1.172
X-RAY DIFFRACTIONc_scangle_it1.72.5
LS refinement shellResolution: 1.6→1.66 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.331 355 11 %
Rwork0.313 2880 -
obs--83.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2PCP.PARWATER.TOP
X-RAY DIFFRACTION3ADP.PARACE.TOP
X-RAY DIFFRACTION4WATER.PARAMPCP.TOP
X-RAY DIFFRACTION5ION.PARAMADP.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.221 / Rfactor Rfree: 0.259
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76
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: 0.331 / % reflection Rfree: 11 % / Rfactor Rwork: 0.313

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