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- PDB-6its: The citrate-bound trimer of chemoreceptor MCP2201 ligand binding ... -

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Basic information

Entry
Database: PDB / ID: 6its
TitleThe citrate-bound trimer of chemoreceptor MCP2201 ligand binding domain
ComponentsMethyl-accepting chemotaxis sensory transducer
KeywordsSIGNALING PROTEIN / methyl-accepting chemotaxis protein / four helix bundle / dicarboxylic organic acid binding
Function / homology
Function and homology information


chemotaxis / transmembrane signaling receptor activity / signal transduction / membrane
Similarity search - Function
: / Chemotaxis methyl-accepting receptor HlyB-like, 4HB MCP domain / Four helix bundle sensory module for signal transduction / Chemotaxis methyl-accepting receptor / 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 ...: / Chemotaxis methyl-accepting receptor HlyB-like, 4HB MCP domain / Four helix bundle sensory module for signal transduction / Chemotaxis methyl-accepting receptor / 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
CITRIC ACID / Methyl-accepting chemotaxis sensory transducer
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsHong, Y. / Li, D.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31870037 China
CitationJournal: Mol.Microbiol. / Year: 2019
Title: The ligand-binding domain of a chemoreceptor from Comamonas testosteroni has a previously unknown homotrimeric structure.
Authors: Hong, Y. / Huang, Z. / Guo, L. / Ni, B. / Jiang, C.Y. / Li, X.J. / Hou, Y.J. / Yang, W.S. / Wang, D.C. / Zhulin, I.B. / Liu, S.J. / Li, D.F.
History
DepositionNov 26, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 10, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 2023Group: 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

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Assembly

Deposited unit
A: Methyl-accepting chemotaxis sensory transducer
B: Methyl-accepting chemotaxis sensory transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6614
Polymers36,2772
Non-polymers3842
Water1,08160
1
A: Methyl-accepting chemotaxis sensory transducer
hetero molecules

A: Methyl-accepting chemotaxis sensory transducer
hetero molecules

A: Methyl-accepting chemotaxis sensory transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9926
Polymers54,4163
Non-polymers5763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area3990 Å2
ΔGint-15 kcal/mol
Surface area22740 Å2
MethodPISA
2
B: Methyl-accepting chemotaxis sensory transducer
hetero molecules

B: Methyl-accepting chemotaxis sensory transducer
hetero molecules

B: Methyl-accepting chemotaxis sensory transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9926
Polymers54,4163
Non-polymers5763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area3680 Å2
ΔGint-20 kcal/mol
Surface area22550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.860, 48.860, 376.152
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-411-

HOH

21A-424-

HOH

31A-426-

HOH

41B-414-

HOH

51B-425-

HOH

61B-428-

HOH

71B-430-

HOH

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Components

#1: Protein Methyl-accepting chemotaxis sensory transducer


Mass: 18138.564 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni (strain CNB-2) (bacteria)
Strain: CNB-2 / Gene: CtCNB1_2201 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: D0IVL9
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 0.1 M SODIUM CITRATE PH 4.4, 14% PEG400, 13% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97907 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 2.5→42.05 Å / Num. obs: 11135 / % possible obs: 95.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 32.6 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.075 / Rrim(I) all: 0.148 / Net I/σ(I): 6.6
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1226 / CC1/2: 0.762 / Rpim(I) all: 0.353 / Rrim(I) all: 0.663 / % possible all: 92.2

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XUB

5xub


Resolution: 2.501→42.049 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 25.59
RfactorNum. reflection% reflectionSelection details
Rfree0.2446 1085 10.11 %Random
Rwork0.1843 ---
obs0.1902 10730 92.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.501→42.049 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2231 0 26 60 2317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082273
X-RAY DIFFRACTIONf_angle_d1.0193077
X-RAY DIFFRACTIONf_dihedral_angle_d27.154865
X-RAY DIFFRACTIONf_chiral_restr0.048375
X-RAY DIFFRACTIONf_plane_restr0.007397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5006-2.61440.28661250.23711111X-RAY DIFFRACTION85
2.6144-2.75220.26211210.21251100X-RAY DIFFRACTION83
2.7522-2.92460.27381280.20851136X-RAY DIFFRACTION88
2.9246-3.15040.30361300.20721171X-RAY DIFFRACTION90
3.1504-3.46730.22841450.1931243X-RAY DIFFRACTION96
3.4673-3.96870.23411440.16711275X-RAY DIFFRACTION99
3.9687-4.99880.20441430.15111316X-RAY DIFFRACTION99
4.9988-42.05450.25541490.19231293X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.57220.47241.73263.17152.81095.2571-0.28770.6999-0.0189-0.61190.3388-0.1342-0.26081.4349-0.27980.3673-0.05240.01890.5669-0.05430.5964-10.501823.4907-35.4238
23.441-0.15251.04932.4540.49868.2491-0.38080.27780.8961-0.4862-0.1872-0.3383-0.48980.20880.50050.3561-0.0125-0.05630.28880.09550.5746-7.312334.4101-26.4909
32.49940.19693.07062.27662.01776.3859-0.72020.10361.1585-0.5168-0.2870.5073-1.0541-0.04560.58380.3716-0.0165-0.0740.3361-0.01420.586-19.820933.5397-29.5805
47.39734.10736.02615.34724.96829.4997-0.3032-0.60970.54160.8153-0.09580.4248-0.0507-0.87480.75460.35790.0813-0.05760.5767-0.17770.5873-18.412534.1076-9.8192
54.25180.00231.0435.25822.31247.12010.2230.6178-0.134-0.9076-0.3027-0.25170.5327-0.12490.08190.39370.06680.06260.28970.07860.3178-18.88518.9735-40.1986
61.3529-1.2509-2.20173.0413.16574.2411.62150.1242-0.90980.15480.0810.2846-0.3256-0.8944-0.66151.237-0.0763-0.03181.33240.13420.97783.672640.154450.5443
71.31591.99553.39212.01734.99548.21440.29680.017-0.36770.73740.0115-0.1221.59030.9716-0.59250.38270.0535-0.03060.2858-0.01980.4839-2.944839.423526.1646
82.92340.42761.83895.07153.18993.1268-0.1628-0.207-0.61170.4577-0.38610.1930.7149-0.13420.65750.3204-0.03480.0160.23230.04620.4473-9.00131.832223.2021
92.95973.26922.49927.12398.29657.06940.1489-0.2721-0.03130.536-0.59450.70820.6345-1.06510.74760.37160.0210.01740.2981-0.06590.4818-14.5343.049725.6673
105.84682.10633.42838.3284.29119.73130.00720.7465-0.5174-1.0627-0.84061.075-0.304-0.98580.8150.44140.1067-0.13640.4482-0.16530.5192-14.776540.23325.72
115.01490.20332.59344.51152.16496.5659-0.2759-0.73840.12460.7404-0.11180.0411-0.16280.51020.24520.4014-0.00570.03730.42220.06910.2969-1.414249.123636.2702
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 53 through 87 )
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 117 )
3X-RAY DIFFRACTION3chain 'A' and (resid 118 through 151 )
4X-RAY DIFFRACTION4chain 'A' and (resid 152 through 164 )
5X-RAY DIFFRACTION5chain 'A' and (resid 165 through 199 )
6X-RAY DIFFRACTION6chain 'B' and (resid 54 through 59 )
7X-RAY DIFFRACTION7chain 'B' and (resid 60 through 87 )
8X-RAY DIFFRACTION8chain 'B' and (resid 88 through 118 )
9X-RAY DIFFRACTION9chain 'B' and (resid 119 through 150 )
10X-RAY DIFFRACTION10chain 'B' and (resid 151 through 164 )
11X-RAY DIFFRACTION11chain 'B' and (resid 165 through 199 )

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