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- PDB-6er7: CHEMOTAXIS PROTEIN CHEY FROM Pyrococcus horikoshiI -

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Basic information

Entry
Database: PDB / ID: 6er7
TitleCHEMOTAXIS PROTEIN CHEY FROM Pyrococcus horikoshiI
Components120aa long hypothetical chemotaxis protein (CheY)
KeywordsSIGNALING PROTEIN / SIGNAL TRANSDUCTION PROTEIN
Function / homology: / phosphorelay signal transduction system / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / 120aa long hypothetical chemotaxis protein (CheY)
Function and homology information
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsPaithankar, K.S. / Enderle, M.E. / Wirthensohn, D. / Grininger, M. / Oesterhelt, D.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Structure of the archaeal chemotaxis protein CheY in a domain-swapped dimeric conformation.
Authors: Paithankar, K.S. / Enderle, M. / Wirthensohn, D.C. / Miller, A. / Schlesner, M. / Pfeiffer, F. / Rittner, A. / Grininger, M. / Oesterhelt, D.
History
DepositionOct 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 120aa long hypothetical chemotaxis protein (CheY)
B: 120aa long hypothetical chemotaxis protein (CheY)
C: 120aa long hypothetical chemotaxis protein (CheY)


Theoretical massNumber of molelcules
Total (without water)39,5723
Polymers39,5723
Non-polymers00
Water00
1
A: 120aa long hypothetical chemotaxis protein (CheY)

A: 120aa long hypothetical chemotaxis protein (CheY)


Theoretical massNumber of molelcules
Total (without water)26,3812
Polymers26,3812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area5130 Å2
ΔGint-48 kcal/mol
Surface area11450 Å2
MethodPISA
2
B: 120aa long hypothetical chemotaxis protein (CheY)

B: 120aa long hypothetical chemotaxis protein (CheY)


Theoretical massNumber of molelcules
Total (without water)26,3812
Polymers26,3812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_758-x+2,y,-z+31
Buried area4900 Å2
ΔGint-46 kcal/mol
Surface area11890 Å2
MethodPISA
3
C: 120aa long hypothetical chemotaxis protein (CheY)

C: 120aa long hypothetical chemotaxis protein (CheY)


Theoretical massNumber of molelcules
Total (without water)26,3812
Polymers26,3812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_658-x+1,y,-z+31
Buried area4600 Å2
ΔGint-47 kcal/mol
Surface area12080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.160, 65.730, 72.890
Angle α, β, γ (deg.)90.000, 110.940, 90.000
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains A B
21Chains A C
32Chains B C

NCS ensembles :
ID
1
2
3

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Components

#1: Protein 120aa long hypothetical chemotaxis protein (CheY) / CHEMOTAXIS PROTEIN CHEY


Mass: 13190.697 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH0482 / Production host: Escherichia coli (E. coli) / References: UniProt: O58193

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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: 2.9 Å3/Da / Density % sol: 58.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris-HCl 1.2 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.6→34 Å / Num. obs: 107515 / % possible obs: 99.5 % / Redundancy: 7.6 % / CC1/2: 1 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.02 / Rrim(I) all: 0.03 / Net I/σ(I): 38

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Processing

Software
NameVersionClassification
REFMAC5.8.0158 2016/10/03refinement
xia20.3.8data reduction
Aimless0.5.32data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TMY

3tmy


Resolution: 2.62→34.038 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.255 / WRfactor Rwork: 0.203 / SU B: 16.383 / SU ML: 0.315 / Cross valid method: FREE R-VALUE / ESU R: 0.564 / ESU R Free: 0.319
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2675 708 -
Rwork0.212 13464 -
all0.215 --
obs-14172 99.278 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 91.73 Å2
Baniso -1Baniso -2Baniso -3
1--3.336 Å2-0 Å21.269 Å2
2---5.291 Å20 Å2
3---5.921 Å2
Refinement stepCycle: LAST / Resolution: 2.62→34.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2688 0 0 0 2688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192712
X-RAY DIFFRACTIONr_bond_other_d0.0020.022820
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.9973639
X-RAY DIFFRACTIONr_angle_other_deg0.99736555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1745348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02126.56396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.215570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.755159
X-RAY DIFFRACTIONr_chiral_restr0.0990.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022889
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02432
X-RAY DIFFRACTIONr_nbd_refined0.2160.21056
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1490.25106
X-RAY DIFFRACTIONr_nbtor_refined0.1640.22582
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.23010
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0490.246
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1750.234
X-RAY DIFFRACTIONr_nbd_other0.1920.2158
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1030.22
X-RAY DIFFRACTIONr_mcbond_it6.8048.8321401
X-RAY DIFFRACTIONr_mcbond_other6.7968.8321400
X-RAY DIFFRACTIONr_mcangle_it9.56813.2531746
X-RAY DIFFRACTIONr_mcangle_other9.5713.2541747
X-RAY DIFFRACTIONr_scbond_it7.2099.5791311
X-RAY DIFFRACTIONr_scbond_other7.2079.5791312
X-RAY DIFFRACTIONr_scangle_it10.77414.0581893
X-RAY DIFFRACTIONr_scangle_other10.77114.0581894
X-RAY DIFFRACTIONr_lrange_it12.981104.8942852
X-RAY DIFFRACTIONr_lrange_other12.981104.912853
X-RAY DIFFRACTIONr_ncsr_local_group_10.1030.056704
X-RAY DIFFRACTIONr_ncsr_local_group_20.110.056696
X-RAY DIFFRACTIONr_ncsr_local_group_30.1130.056630
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
2.62-2.6880.39500.362960102698.44050.326
2.688-2.7610.386440.32980103099.41750.279
2.761-2.840.397460.33692198098.67350.297
2.84-2.9270.411420.31991596399.37690.269
2.927-3.0220.392600.2987293999.25450.252
3.022-3.1280.385360.27485589999.11010.24
3.128-3.2450.327260.2938288541000.257
3.245-3.3760.296390.28181185699.29910.254
3.376-3.5240.344380.25575980599.00620.235
3.524-3.6940.316490.25770375999.07770.242
3.694-3.8920.267410.23469474099.32430.223
3.892-4.1240.274350.18366870599.71630.177
4.124-4.4050.195370.16462065999.69650.164
4.405-4.7510.224350.15856660299.83390.164
4.751-5.1940.196440.16352957499.82580.171
5.194-5.790.203230.1774915141000.182
5.79-6.6540.292180.19844045999.78210.209
6.654-8.0730.221200.16536738999.48590.182
8.073-11.1090.155120.13329831299.3590.158
11.109-34.0380.336130.24118720199.50250.281

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