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- PDB-6c40: CheY41PyTyrD54K from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 6c40
TitleCheY41PyTyrD54K from Thermotoga maritima
ComponentsChemotaxis protein CheY
KeywordsSIGNALING PROTEIN / CheY / Chemotaxis / PyTyr
Function / homology
Function and homology information


archaeal or bacterial-type flagellum-dependent cell motility / phosphorelay signal transduction system / chemotaxis / metal ion binding / cytoplasm
Similarity search - Function
: / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily
Similarity search - Domain/homology
COPPER (II) ION / Chemotaxis protein CheY
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsMerz, G.E. / Muok, A.R. / Crane, B.R.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM066775 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM079679 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122535 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103521 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008267 United States
CitationJournal: J Phys Chem B / Year: 2018
Title: Site-Specific Incorporation of a Cu2+Spin Label into Proteins for Measuring Distances by Pulsed Dipolar Electron Spin Resonance Spectroscopy.
Authors: Merz, G.E. / Borbat, P.P. / Muok, A.R. / Srivastava, M. / Bunck, D.N. / Freed, J.H. / Crane, B.R.
History
DepositionJan 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.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.ptnr1_symmetry / _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.ptnr2_symmetry / _struct_conn_type.id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Chemotaxis protein CheY
D: Chemotaxis protein CheY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5588
Polymers26,1772
Non-polymers3816
Water1448
1
B: Chemotaxis protein CheY
hetero molecules

D: Chemotaxis protein CheY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5588
Polymers26,1772
Non-polymers3816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area990 Å2
ΔGint-48 kcal/mol
Surface area11540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.634, 34.816, 58.547
Angle α, β, γ (deg.)98.800, 104.420, 100.330
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain B
21chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain BB2 - 204
211chain DD2 - 204

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Components

#1: Protein Chemotaxis protein CheY


Mass: 13088.591 Da / Num. of mol.: 2 / Mutation: E41PyTyr, D54K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: cheY, TM_0700 / Production host: Escherichia coli (E. coli) / References: UniProt: Q56312
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: HEPES pH 7, ammonium sulfate, PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 6625 / % possible obs: 55.3 % / Redundancy: 2 % / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.134 / Rrim(I) all: 0.233 / Χ2: 3.536 / Net I/σ(I): 4.6 / Num. measured all: 19710
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2% possible allRmerge(I) obsRpim(I) allRrim(I) allΧ2
1.94-1.971500.6935.5
1.97-2.011687.5
2.01-2.05110411.4
2.05-2.09112213.20.5030.5030.7110.034
2.09-2.1411380.14315.70.5730.5730.810.43
2.14-2.1812150.56422.91.8561.8562.6250.369
2.18-2.241.12470.56427.60.4950.4780.6890.279
2.24-2.31.12940.00232.51.4761.3171.9860.748
2.3-2.371.13880.43942.51.1791.061.5910.465
2.37-2.441.25070.47355.20.5650.5070.7630.387
2.44-2.531.46010.342670.6950.6160.9330.492
2.53-2.631.56940.63876.60.5610.4840.7440.657
2.63-2.751.77350.69380.50.6390.5310.8360.675
2.75-2.91.97810.60985.10.5490.4460.7120.806
2.9-3.082.28580.64593.80.4690.370.6011.167
3.08-3.322.58630.85894.80.3450.2520.431.746
3.32-3.652.68340.8793.10.2710.1940.3363.052
3.65-4.182.68680.90995.10.2010.1440.2494.218
4.18-5.262.68440.94493.50.1520.1090.1885.407
5.26-502.68420.93292.10.1620.1110.1979.307

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 4TMY

4tmy


Resolution: 2.7→33.507 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 35.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2955 635 10.18 %
Rwork0.2171 5604 -
obs0.225 6239 91.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.94 Å2 / Biso mean: 67.2719 Å2 / Biso min: 38.88 Å2
Refinement stepCycle: final / Resolution: 2.7→33.507 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1782 0 6 8 1796
Biso mean--95.09 61.26 -
Num. residues----236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161827
X-RAY DIFFRACTIONf_angle_d1.7572418
X-RAY DIFFRACTIONf_chiral_restr0.081288
X-RAY DIFFRACTIONf_plane_restr0.009304
X-RAY DIFFRACTIONf_dihedral_angle_d6.4251124
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B1048X-RAY DIFFRACTION13.625TORSIONAL
12D1048X-RAY DIFFRACTION13.625TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7002-2.90860.37571180.27791037115584
2.9086-3.20110.3571280.26381135126394
3.2011-3.66380.31261270.22741148127593
3.6638-4.61410.27621350.20631148128395
4.6141-33.50960.27531270.20071136126392

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