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- PDB-5xub: The citrate-bound trimer of chemoreceptor MCP2201 ligand binding ... -

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Basic information

Entry
Database: PDB / ID: 5xub
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: 2.5 Å
AuthorsHong, Y. / Li, D.F. / Wang, D.C.
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
DepositionJun 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 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 1.2Nov 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
Water1,71195
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_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area3720 Å2
ΔGint-20 kcal/mol
Surface area22570 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_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area3670 Å2
ΔGint-17 kcal/mol
Surface area22000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.400, 49.400, 406.342
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-421-

HOH

21A-440-

HOH

31B-435-

HOH

41B-446-

HOH

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Components

#1: Protein Methyl-accepting chemotaxis sensory transducer


Mass: 18138.564 Da / Num. of mol.: 2 / Fragment: UNP residues 46-203
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


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


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium citrate pH 4.4, 14% PEG 400, 13% Ethylene glycol
PH range: 4.0 - 4.8

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.5→45.15 Å / Num. obs: 12095 / % possible obs: 94.5 % / Redundancy: 2.3 % / Biso Wilson estimate: 34.685 Å2 / CC1/2: 0.953 / Rmerge(I) obs: 0.152 / Net I/σ(I): 4.3
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1744 / CC1/2: 0.791 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
iMOSFLMdata processing
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XUD

5xud
PDB Unreleased entry


Resolution: 2.5→41.864 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.38
RfactorNum. reflection% reflectionSelection details
Rfree0.2567 1201 9.93 %Random
Rwork0.2034 ---
obs0.2087 12091 94.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→41.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2167 0 26 95 2288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072209
X-RAY DIFFRACTIONf_angle_d0.9832990
X-RAY DIFFRACTIONf_dihedral_angle_d17.1061398
X-RAY DIFFRACTIONf_chiral_restr0.048365
X-RAY DIFFRACTIONf_plane_restr0.005384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.60020.29291380.24671215X-RAY DIFFRACTION94
2.6002-2.71850.32341320.23191211X-RAY DIFFRACTION95
2.7185-2.86180.27881300.23731209X-RAY DIFFRACTION95
2.8618-3.0410.29251340.22811211X-RAY DIFFRACTION94
3.041-3.27570.3331360.24381247X-RAY DIFFRACTION96
3.2757-3.60520.28271270.20621215X-RAY DIFFRACTION95
3.6052-4.12650.22661410.17111230X-RAY DIFFRACTION96
4.1265-5.19740.20951350.16641193X-RAY DIFFRACTION94
5.1974-41.86940.20181280.18761159X-RAY DIFFRACTION89
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)
10.82760.0479-0.49841.9374-1.81735.0252-0.0013-0.18830.22360.5815-0.17810.0077-0.5927-0.11750.15040.3502-0.0193-0.03130.2364-0.04740.42575.5702-7.668628.8585
21.45090.5309-0.78172.3894-3.78496.3021-0.0833-0.29140.22210.4861-0.56-0.9037-0.45611.00540.47250.3159-0.0067-0.08440.30250.0430.455114.6662-15.141328.2687
31.85180.5013-2.11021.4798-1.43854.76450.12640.37010.0106-0.1747-0.4896-0.72770.02230.70480.40280.2960.00440.14430.40050.15710.529814.7282-12.15318.3039
42.779-0.1253-1.07822.40380.09282.51550.1624-0.4460.32760.5229-0.023-0.3015-0.254-0.3714-0.22210.33850.0367-0.02330.3584-0.06430.18461.2259-20.943839.5358
51.8182-0.3616-2.78242.3017-2.05827.5923-0.22780.43470.0073-0.5059-0.11650.2683-0.1695-0.9345-0.1820.3086-0.0466-0.06050.3551-0.01430.436811.04653.6898-30.1455
62.2090.9873-2.3381.0177-1.69667.1173-0.25250.5482-0.3633-0.11530.2139-0.25090.4063-0.81310.270.2876-0.04980.04720.2912-0.03470.4057.6054-6.1027-24.6105
71.09851.3035-3.55441.649-2.87557.4679-0.544-0.104-0.6859-0.73580.02130.02821.40680.68310.38450.2911-0.02230.07380.331-0.03560.550120.4189-5.1378-27.0367
80.3630.2504-1.73244.0393-1.79999.0483-0.0813-1.3008-0.88010.5323-0.0386-0.12780.20721.44021.18680.23380.05640.00690.33090.33390.605317.8521-6.6828-7.0727
92.45970.115-0.13642.0663-1.36284.82540.28910.5183-0.2259-0.48610.04050.4049-0.38050.2683-0.35740.38420.0017-0.06070.303-0.05530.280919.32198.7435-36.3767
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 57 through 118 )
2X-RAY DIFFRACTION2chain 'A' and (resid 119 through 150 )
3X-RAY DIFFRACTION3chain 'A' and (resid 151 through 164 )
4X-RAY DIFFRACTION4chain 'A' and (resid 165 through 200 )
5X-RAY DIFFRACTION5chain 'B' and (resid 57 through 87 )
6X-RAY DIFFRACTION6chain 'B' and (resid 88 through 118 )
7X-RAY DIFFRACTION7chain 'B' and (resid 119 through 150 )
8X-RAY DIFFRACTION8chain 'B' and (resid 151 through 164 )
9X-RAY DIFFRACTION9chain 'B' and (resid 165 through 197 )

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