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

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Basic information

Entry
Database: PDB / ID: 6exr
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: 2.16 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
DepositionNov 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 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 1.2Jan 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)
D: 120aa long hypothetical chemotaxis protein (CheY)
E: 120aa long hypothetical chemotaxis protein (CheY)
F: 120aa long hypothetical chemotaxis protein (CheY)


Theoretical massNumber of molelcules
Total (without water)79,1446
Polymers79,1446
Non-polymers00
Water00
1
A: 120aa long hypothetical chemotaxis protein (CheY)
B: 120aa long hypothetical chemotaxis protein (CheY)
C: 120aa long hypothetical chemotaxis protein (CheY)
D: 120aa long hypothetical chemotaxis protein (CheY)
E: 120aa long hypothetical chemotaxis protein (CheY)
F: 120aa long hypothetical chemotaxis protein (CheY)

A: 120aa long hypothetical chemotaxis protein (CheY)
B: 120aa long hypothetical chemotaxis protein (CheY)
C: 120aa long hypothetical chemotaxis protein (CheY)
D: 120aa long hypothetical chemotaxis protein (CheY)
E: 120aa long hypothetical chemotaxis protein (CheY)
F: 120aa long hypothetical chemotaxis protein (CheY)


Theoretical massNumber of molelcules
Total (without water)158,28812
Polymers158,28812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area35860 Å2
ΔGint-340 kcal/mol
Surface area64800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.140, 124.370, 73.420
Angle α, β, γ (deg.)90.000, 111.750, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains A B
21Chains A C
31Chains A D
41Chains A E
51Chains A F
61Chains B C
71Chains B D
81Chains B E
91Chains B F
101Chains C D
111Chains C E
121Chains C F
131Chains D E
141Chains D F
151Chains E F

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Components

#1: Protein
120aa long hypothetical chemotaxis protein (CheY)


Mass: 13190.697 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
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: 2.92 Å3/Da / Density % sol: 57.93 %
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 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.16→68.19 Å / Num. obs: 47836 / % possible obs: 98.2 % / Redundancy: 7.4 % / Biso Wilson estimate: 40.95 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.023 / Rrim(I) all: 0.062 / Net I/σ(I): 22.8
Reflection shellResolution: 2.16→2.2 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1953 / CC1/2: 0.56 / Rpim(I) all: 0.6 / Rrim(I) all: 1.6 / % possible all: 82

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Processing

Software
NameVersionClassification
REFMAC5.8.0158 2016/10/03refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1u0s

1u0s


Resolution: 2.16→68.193 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.25 / WRfactor Rwork: 0.222 / SU B: 7.515 / SU ML: 0.184 / Cross valid method: FREE R-VALUE / ESU R: 0.252 / ESU R Free: 0.208
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2751 2338 -
Rwork0.242 45497 -
all0.244 --
obs-47835 98.19 %
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: 54.307 Å2
Baniso -1Baniso -2Baniso -3
1--0.263 Å20 Å21.163 Å2
2---0.561 Å2-0 Å2
3----0.078 Å2
Refinement stepCycle: LAST / Resolution: 2.16→68.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5344 0 0 0 5344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195388
X-RAY DIFFRACTIONr_bond_other_d0.0020.025614
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.9927218
X-RAY DIFFRACTIONr_angle_other_deg1.01313042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0815690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78426.526190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.545151136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6761518
X-RAY DIFFRACTIONr_chiral_restr0.0990.2878
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025702
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02860
X-RAY DIFFRACTIONr_nbd_refined0.2250.21974
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1540.210156
X-RAY DIFFRACTIONr_nbtor_refined0.1650.25206
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.26024
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.262
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1240.226
X-RAY DIFFRACTIONr_nbd_other0.1960.2164
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0620.22
X-RAY DIFFRACTIONr_mcbond_it4.8245.0392784
X-RAY DIFFRACTIONr_mcbond_other4.8215.0392783
X-RAY DIFFRACTIONr_mcangle_it6.3717.5423466
X-RAY DIFFRACTIONr_mcangle_other6.377.5423467
X-RAY DIFFRACTIONr_scbond_it6.0675.7342604
X-RAY DIFFRACTIONr_scbond_other6.0665.7342605
X-RAY DIFFRACTIONr_scangle_it9.0048.2823752
X-RAY DIFFRACTIONr_scangle_other9.0038.2823753
X-RAY DIFFRACTIONr_lrange_it10.7359.6255605
X-RAY DIFFRACTIONr_lrange_other10.72959.6285606
X-RAY DIFFRACTIONr_ncsr_local_group_10.1020.056550
X-RAY DIFFRACTIONr_ncsr_local_group_20.0920.056552
X-RAY DIFFRACTIONr_ncsr_local_group_30.0880.056648
X-RAY DIFFRACTIONr_ncsr_local_group_40.1080.056478
X-RAY DIFFRACTIONr_ncsr_local_group_50.0660.056760
X-RAY DIFFRACTIONr_ncsr_local_group_60.1140.056438
X-RAY DIFFRACTIONr_ncsr_local_group_70.1030.056576
X-RAY DIFFRACTIONr_ncsr_local_group_80.1150.056422
X-RAY DIFFRACTIONr_ncsr_local_group_90.1030.056554
X-RAY DIFFRACTIONr_ncsr_local_group_100.1040.056518
X-RAY DIFFRACTIONr_ncsr_local_group_110.0930.056548
X-RAY DIFFRACTIONr_ncsr_local_group_120.0940.056530
X-RAY DIFFRACTIONr_ncsr_local_group_130.110.056476
X-RAY DIFFRACTIONr_ncsr_local_group_140.0970.056602
X-RAY DIFFRACTIONr_ncsr_local_group_150.1070.056486
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
2.16-2.2160.3771400.352818354883.37090.343
2.216-2.2770.4361590.3853107352492.67880.378
2.277-2.3430.4361710.3263221340299.70610.294
2.343-2.4150.3171590.2923154331499.96980.257
2.415-2.4940.3341540.2913035319699.7810.251
2.494-2.5810.3431490.299294230911000.254
2.581-2.6780.3521320.2792885301899.96690.234
2.678-2.7880.3121450.2582702284999.92980.218
2.788-2.9110.2821450.2712627277499.92790.235
2.911-3.0530.3721210.2762535265799.96240.248
3.053-3.2180.3081410.29236725081000.265
3.218-3.4130.3551270.272246237699.87370.254
3.413-3.6480.251110.2612139225299.91120.248
3.648-3.9390.286980.241199220901000.234
3.939-4.3140.221060.191181719231000.189
4.314-4.820.175770.1591669174799.94280.163
4.82-5.5610.217740.197145615301000.2
5.561-6.80.351530.22125813111000.221
6.8-9.5690.144450.165972102099.70590.177
9.569-68.1930.141310.2145555861000.235

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