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- PDB-8f7n: Crystal structure of chemoreceptor McpZ ligand sensing domain -

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Basic information

Entry
Database: PDB / ID: 8f7n
TitleCrystal structure of chemoreceptor McpZ ligand sensing domain
ComponentsMethyl-accepting chemotaxis protein
KeywordsSIGNALING PROTEIN / MCP (Methyl-accepting chemotaxis protein) / Chemotaxis / Chemoreceptor
Function / homology
Function and homology information


signal transduction / membrane
Similarity search - Function
Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain
Similarity search - Domain/homology
YTTERBIUM (III) ION / Methyl-accepting chemotaxis protein
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsSalar, S. / Schubot, F.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1817652 United States
Department of Energy (DOE, United States)W-31-109-ENG-38 United States
CitationJournal: Proteins / Year: 2023
Title: The structural analysis of the periplasmic domain of Sinorhizobium meliloti chemoreceptor McpZ reveals a novel fold and suggests a complex mechanism of transmembrane signaling.
Authors: Salar, S. / Ball, N.E. / Baaziz, H. / Nix, J.C. / Sobe, R.C. / Compton, K.K. / Zhulin, I.B. / Brown, A.M. / Scharf, B.E. / Schubot, F.D.
History
DepositionNov 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,53311
Polymers41,8021
Non-polymers1,73010
Water1629
1
A: Methyl-accepting chemotaxis protein
hetero molecules

A: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,06522
Polymers83,6042
Non-polymers3,46120
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y+1/2,-z+1/41
MethodPISA
Unit cell
Length a, b, c (Å)184.330, 184.330, 113.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-501-

YB

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Components

#1: Protein Methyl-accepting chemotaxis protein


Mass: 41802.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Gene: CN211_06960 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8B3MS64
#2: Chemical
ChemComp-YB / YTTERBIUM (III) ION


Mass: 173.040 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Yb
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 295.15 K / Method: vapor diffusion, sitting drop
Details: Lanthanides, MOPSO, Bis-Tris pH 6.5, and Precipitant Mix 8 (PEG 20000, Trimethylpropane, NDSB 195)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jul 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.54→46.6 Å / Num. obs: 32346 / % possible obs: 99.9 % / Redundancy: 20 % / Biso Wilson estimate: 75.86 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.031 / Rrim(I) all: 0.169 / Χ2: 0.84 / Net I/σ(I): 17.8
Reflection shellResolution: 2.54→2.65 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 3873 / CC1/2: 0.41 / Χ2: 0.64 / % possible all: 100

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Processing

Software
NameVersionClassification
iMOSFLMv7.4.0data reduction
PHENIXv1.19.2-4158refinement
PDB_EXTRACTdata extraction
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.7→46.6 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2596 2517 4.92 %
Rwork0.2444 --
obs0.2452 26500 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2767 0 10 9 2786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012797
X-RAY DIFFRACTIONf_angle_d1.2063770
X-RAY DIFFRACTIONf_dihedral_angle_d19.5881041
X-RAY DIFFRACTIONf_chiral_restr0.048443
X-RAY DIFFRACTIONf_plane_restr0.013492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.750.37011340.37012690X-RAY DIFFRACTION99
2.75-2.810.37171400.35192686X-RAY DIFFRACTION99
2.81-2.870.36761422677X-RAY DIFFRACTION100
2.87-2.940.33111500.3272723X-RAY DIFFRACTION100
2.94-3.010.331340.31352702X-RAY DIFFRACTION100
3.01-3.090.35991520.29392694X-RAY DIFFRACTION100
3.09-3.180.32911710.29592677X-RAY DIFFRACTION100
3.18-3.280.29851200.28612712X-RAY DIFFRACTION100
3.28-3.40.3561430.29622720X-RAY DIFFRACTION100
3.4-3.540.28581300.24942708X-RAY DIFFRACTION100
3.54-3.70.23651420.23582673X-RAY DIFFRACTION100
3.7-3.890.26681380.22592716X-RAY DIFFRACTION100
3.89-4.140.23121282700X-RAY DIFFRACTION100
4.14-4.460.26431520.20792708X-RAY DIFFRACTION100
4.46-4.90.25891280.21352717X-RAY DIFFRACTION100
4.9-5.610.25331442697X-RAY DIFFRACTION100
5.62-7.070.2831332717X-RAY DIFFRACTION100
7.07-46.60.18021362698X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 75.1245 Å / Origin y: 45.3564 Å / Origin z: 16.535 Å
111213212223313233
T0.5049 Å20.0371 Å2-0.0122 Å2-0.5916 Å20.2165 Å2--0.4967 Å2
L4.2567 °21.7444 °2-1.4187 °2-1.6972 °2-0.3859 °2--1.012 °2
S-0.0577 Å °0.232 Å °-0.0369 Å °-0.0895 Å °0.0591 Å °0.1242 Å °0.0181 Å °-0.2632 Å °0.0339 Å °
Refinement TLS groupSelection details: all

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