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- PDB-1a0o: CHEY-BINDING DOMAIN OF CHEA IN COMPLEX WITH CHEY -

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Basic information

Entry
Database: PDB / ID: 1a0o
TitleCHEY-BINDING DOMAIN OF CHEA IN COMPLEX WITH CHEY
Components
  • CHEA
  • CHEY
KeywordsCHEMOTAXIS / BACTERIAL CHEMOTAXIS / SIGNAL TRANSDUCTION / TWO-COMPONENT SYSTEM / HISTIDINE KINASE / RESPONSE REGULATOR
Function / homology
Function and homology information


negative regulation of protein modification process / methyl accepting chemotaxis protein complex / positive regulation of post-translational protein modification / bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / protein histidine kinase activity / bacterial-type flagellum ...negative regulation of protein modification process / methyl accepting chemotaxis protein complex / positive regulation of post-translational protein modification / bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / protein histidine kinase activity / bacterial-type flagellum / regulation of chemotaxis / thermotaxis / internal peptidyl-lysine acetylation / phosphorelay response regulator activity / protein acetylation / histidine kinase / phosphorelay sensor kinase activity / acetyltransferase activity / phosphorelay signal transduction system / establishment of localization in cell / chemotaxis / phosphorylation / magnesium ion binding / signal transduction / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
CheY-binding domain of CheA / CheY binding / CheY binding / 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 ...CheY-binding domain of CheA / CheY binding / CheY binding / 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, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / 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 / Histidine kinase/HSP90-like ATPase superfamily / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Chemotaxis protein CheY / Chemotaxis protein CheA / Chemotaxis protein CheY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS, DENSITY MODIFICATION, MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsChinardet, N. / Welch, M. / Mourey, L. / Birck, C. / Samama, J.P.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Structure of the CheY-binding domain of histidine kinase CheA in complex with CheY.
Authors: Welch, M. / Chinardet, N. / Mourey, L. / Birck, C. / Samama, J.P.
History
DepositionDec 5, 1997Processing site: BNL
Revision 1.0Dec 30, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_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

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Assembly

Deposited unit
A: CHEY
B: CHEA
C: CHEY
D: CHEA
E: CHEY
F: CHEA
G: CHEY
H: CHEA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,16612
Polymers113,9468
Non-polymers2204
Water0
1
A: CHEY
B: CHEA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5413
Polymers28,4872
Non-polymers551
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: CHEY
D: CHEA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5413
Polymers28,4872
Non-polymers551
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: CHEY
F: CHEA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5413
Polymers28,4872
Non-polymers551
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: CHEY
H: CHEA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5413
Polymers28,4872
Non-polymers551
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.900, 156.970, 65.970
Angle α, β, γ (deg.)90.00, 91.70, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.965495, -0.041515, -0.25709), (-0.093978, 0.976233, 0.195287), (0.242873, 0.212709, -0.94645)31.5675, 70.2111, 21.9539
2given(-0.99981, 0.012638, 0.014842), (-0.012499, -0.999877, 0.009421), (0.01496, 0.009234, 0.999845)49.9671, 59.7521, 32.9154
3given(0.961545, 0.053144, 0.269455), (0.109126, -0.974258, -0.197265), (0.252035, 0.219083, -0.942592)20.4537, 146.5614, 54.7019

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Components

#1: Protein
CHEY


Mass: 13981.136 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P06143, UniProt: P0AE67*PLUS
#2: Protein
CHEA /


Mass: 14505.375 Da / Num. of mol.: 4 / Fragment: CHEA 124-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli)
References: UniProt: P07363, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 44 %
Crystal growpH: 5.5
Details: PROTEIN WAS CRYSTALLIZED FROM 20% PEG MME 5K, 0.1 M MALONIC ACID, 0.1 M MES BUFFER PH 5.5, 0.02 M DTT, 0.01 M MANGANESE CHLORIDE
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.9 / Method: vapor diffusion / Details: drop was mixed with an equal volume of reservoir
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
225 mMTris-HCl1drop
3100 mMMES1reservoir
4100 mMmalonic acid1reservoir
520 mMdithiothreitol1reservoir
610 mM1reservoirMnCl2
710 mM1reservoirKCl

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.95→29 Å / Num. obs: 41612 / % possible obs: 92 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 9.5
Reflection shellResolution: 2.95→3.03 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.099 / Mean I/σ(I) obs: 6.8 / % possible all: 86.4
Reflection shell
*PLUS
% possible obs: 86.4 %

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Processing

Software
NameVersionClassification
SHARPphasing
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
SCALAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIRAS, DENSITY MODIFICATION, MOLECULAR REPLACEMENT
Starting model: 1CHN

1chn


Resolution: 2.95→27 Å / Rfactor Rfree error: 0.0072 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0
Details: NCS CONSTRAINTS WERE ONLY APPLIED IN THE FIRST REFINEMENT CYCLES ONE OF THE CONSTRUCTS USED FOR THE CRYSTAL STRUCTURE DETERMINATION CONSISTS OF THE CHEY-BINDING DOMAIN OF CHEA FLANKED BY ...Details: NCS CONSTRAINTS WERE ONLY APPLIED IN THE FIRST REFINEMENT CYCLES ONE OF THE CONSTRUCTS USED FOR THE CRYSTAL STRUCTURE DETERMINATION CONSISTS OF THE CHEY-BINDING DOMAIN OF CHEA FLANKED BY DOMAIN LINKERS (CHEA124-257). IN THE FINAL MODEL, EACH MOLECULE OF THE COMPLEX COMPRISES 128 RESIDUES IN CHEY AND AN ACTIVE SITE-BOUND MN2+, AND 70 RESIDUES IN CHEA124-257 SPANNING THE REGION 159-228. NO ELECTRON DENSITY COULD BE ASSIGNED TO THE REMAINING RESIDUES IN CHEA124-257.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1073 4.65 %SHELLS
Rwork0.187 ---
obs0.187 20984 90.92 %-
Displacement parametersBiso mean: 33.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.29 Å
Refinement stepCycle: LAST / Resolution: 2.95→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5965 0 4 0 5969
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: UNRESTRAINED
LS refinement shellResolution: 2.95→3.08 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.379 143 4.95 %
Rwork0.275 2413 -
obs--88.43 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2

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