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- PDB-9kup: Crystal structure of MCP2201LBD -

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Basic information

Entry
Database: PDB / ID: 9kup
TitleCrystal structure of MCP2201LBD
ComponentsMethyl-accepting chemotaxis sensory transducer
KeywordsHYDROLASE / Complex
Function / homology
Function and homology information


: / 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 ...: / 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
D-MALATE / Methyl-accepting chemotaxis sensory transducer
Similarity search - Component
Biological speciesComamonas thiooxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCui, R. / Li, D.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)111111 China
CitationJournal: Int J Mol Sci / Year: 2025
Title: Insights into Chemoreceptor MCP2201-Sensing D-Malate.
Authors: Cui, R. / Li, J. / Hong, Y. / Guo, L. / Wang, Y.H. / Bai, Y.F. / Li, D.F.
History
DepositionDec 4, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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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)40,0777
Polymers39,5252
Non-polymers5525
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-40 kcal/mol
Surface area12620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.800, 59.800, 158.201
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Methyl-accepting chemotaxis sensory transducer


Mass: 19762.424 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas thiooxydans (bacteria) / Gene: CtCNB1_2201 / Production host: Escherichia coli (E. coli) / References: UniProt: A0ABF7PFR0
#2: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 41.31 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: 1.8 M Ammonium sulfate, 5% Glycerol

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Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2013
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.4→43.37 Å / Num. obs: 55393 / % possible obs: 84.6 % / Redundancy: 16.4 % / Rmerge(I) obs: 0.578 / Net I/σ(I): 18.3
Reflection shellResolution: 1.4→1.42 Å / Rmerge(I) obs: 0.8131 / Num. unique obs: 734 / % possible all: 23.5

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata scaling
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→43.328 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.25 / Phase error: 16.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1848 1980 3.92 %RANDOM
Rwork0.1638 ---
obs0.1647 50566 94.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→43.328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 34 397 2461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132093
X-RAY DIFFRACTIONf_angle_d1.2822832
X-RAY DIFFRACTIONf_dihedral_angle_d16.3561319
X-RAY DIFFRACTIONf_chiral_restr0.078345
X-RAY DIFFRACTIONf_plane_restr0.008361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53750.1917970.18552374X-RAY DIFFRACTION65
1.5375-1.57910.22321090.16862756X-RAY DIFFRACTION77
1.5791-1.62560.17681290.16273141X-RAY DIFFRACTION87
1.6256-1.6780.23231360.173390X-RAY DIFFRACTION95
1.678-1.7380.21331510.17173631X-RAY DIFFRACTION99
1.738-1.80760.21911500.17673632X-RAY DIFFRACTION100
1.8076-1.88990.22061490.18033654X-RAY DIFFRACTION100
1.8899-1.98950.20191480.16643670X-RAY DIFFRACTION100
1.9895-2.11410.1711490.15693627X-RAY DIFFRACTION100
2.1141-2.27740.16771450.15083660X-RAY DIFFRACTION100
2.2774-2.50650.18481550.16153703X-RAY DIFFRACTION100
2.5065-2.86920.16661480.16753707X-RAY DIFFRACTION100
2.8692-3.61460.20061550.1623731X-RAY DIFFRACTION100
3.6146-43.3280.16461590.16153910X-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)
10.48610.21990.02610.06360.16870.3162-0.03320.0169-0.14410.01930.0668-0.0335-0.0048-0.06660.02480.10130.01260.03310.10950.02690.147817.71045.781818.2056
2-0.0908-0.2261-0.06270.30410.01480.2826-0.05040.07270.0099-0.06790.11310.1365-0.0008-0.1319-0.0260.1206-0.0172-0.01170.17120.05850.142712.700911.552511.095
30.3608-0.14730.02220.33390.2110.6053-0.0198-0.01360.07390.0713-0.01560.1329-0.0631-0.0795-0.16470.110.01910.0120.11950.02820.119410.071419.587720.5237
40.22370.1729-0.05770.0912-0.01290.4614-0.01180.0252-0.13290.04710.0847-0.22920.07910.03230.00230.12830.0303-0.01290.1265-0.01780.170917.82753.222426.3804
50.2404-0.16830.10360.1308-0.06680.1767-0.0295-0.0214-0.00810.08130.06930.0977-0.0334-0.02360.00290.11150.01060.02350.0860.00150.09128.588711.08314.0776
60.1560.04250.04180.0613-0.24450.2676-0.0199-0.041-0.01160.12940.00930.0016-0.03930.0428-00.13610.0131-0.01590.1129-0.0050.08836.87655.672618.4856
70.02650.0010.05730.4571-0.01080.1551-0.00710.02150.0269-0.02510.0169-0.1204-0.02460.04220.05140.0965-0.00810.02470.08370.00310.09937.22314.68644.4119
80.0894-0.2166-0.17620.15320.14750.1893-0.0192-0.0227-0.0187-0.07260.05630.05920.0539-0.0439-00.1058-0.01490.00350.0849-0.0010.086930.1412-0.18527.1718
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 57 through 87 )
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 121 )
3X-RAY DIFFRACTION3chain 'A' and (resid 122 through 164 )
4X-RAY DIFFRACTION4chain 'A' and (resid 165 through 192 )
5X-RAY DIFFRACTION5chain 'B' and (resid 58 through 97 )
6X-RAY DIFFRACTION6chain 'B' and (resid 98 through 121 )
7X-RAY DIFFRACTION7chain 'B' and (resid 122 through 164 )
8X-RAY DIFFRACTION8chain 'B' and (resid 165 through 188 )

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