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- PDB-7wrm: The malate-bound dimer of chemoreceptor MCP2201 ligand binding domain -

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Basic information

Entry
Database: PDB / ID: 7wrm
TitleThe malate-bound dimer 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
(2S)-2-hydroxybutanedioic acid / Methyl-accepting chemotaxis sensory transducer
Similarity search - Component
Biological speciesComamonas testosteroni CNB-2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHong, Y. / Guo, L. / Li, D.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92051101 China
CitationJournal: to be published
Title: The repellent response to malate mediated by chemoreceptor MCP2201 in Comamonas testosteroni CNB-1
Authors: Guo, L. / Li, D.F. / Liu, S.J.
History
DepositionJan 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 4, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)34,1854
Polymers33,9162
Non-polymers2682
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-14 kcal/mol
Surface area13770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.420, 59.840, 98.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Methyl-accepting chemotaxis sensory transducer


Mass: 16958.246 Da / Num. of mol.: 2 / Fragment: UNP residues 57-203
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni 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-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate / Malic acid


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / 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

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.6, 22% PEG 3,350, 5%Glycerol

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.8→42.7 Å / Num. obs: 26227 / % possible obs: 98.8 % / Redundancy: 11.8 % / Biso Wilson estimate: 13.586 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Net I/σ(I): 16.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 3726 / CC1/2: 0.892 / % possible all: 97.6

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIXphasing
PHENIXv.1.14refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XUA

5xua


Resolution: 1.8→42.69 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.33
RfactorNum. reflection% reflectionSelection details
Rfree0.2082 2000 7.64 %Random
Rwork0.1803 ---
obs0.1824 26184 98.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→42.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2168 0 18 203 2389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042220
X-RAY DIFFRACTIONf_angle_d0.6573001
X-RAY DIFFRACTIONf_dihedral_angle_d14.3371417
X-RAY DIFFRACTIONf_chiral_restr0.038369
X-RAY DIFFRACTIONf_plane_restr0.004386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.45161380.46981671X-RAY DIFFRACTION98
1.845-1.89490.36951400.31751684X-RAY DIFFRACTION97
1.8949-1.95070.24631410.21231705X-RAY DIFFRACTION99
1.9507-2.01360.21541400.18581692X-RAY DIFFRACTION98
2.0136-2.08560.23651390.17921683X-RAY DIFFRACTION98
2.0856-2.16910.20511400.16241699X-RAY DIFFRACTION98
2.1691-2.26780.22821420.16391714X-RAY DIFFRACTION98
2.2678-2.38740.18631430.16541729X-RAY DIFFRACTION99
2.3874-2.53690.20871410.1691712X-RAY DIFFRACTION99
2.5369-2.73280.19931450.16871744X-RAY DIFFRACTION99
2.7328-3.00770.19231420.16531728X-RAY DIFFRACTION99
3.0077-3.44280.18281460.16791761X-RAY DIFFRACTION99
3.4428-4.33690.17351480.15821781X-RAY DIFFRACTION99
4.3369-42.690.21291550.18771881X-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)
14.44482.75160.60934.24730.37981.66210.11760.1766-0.00180.13650.01750.0670.01460.0735-0.11770.12750.07420.00240.1505-0.01970.1019-0.8275-0.3377-13.5454
27.75866.29984.16345.22713.38143.1410.09460.3148-0.4019-0.14640.2112-0.4145-0.08170.3187-0.410.17130.03390.00760.2333-0.07660.204810.12690.8284-15.6196
35.89727.02063.96398.26034.65732.460.35280.0183-0.66370.48560.0496-0.51130.39130.1694-0.34580.26330.0285-0.0770.2137-0.03290.26796.6088-8.0342-6.8077
42.58961.93821.14366.06182.48182.2195-0.00020.06510.0306-0.1103-0.06890.40490.057-0.0073-0.00420.14140.0331-0.02880.1663-0.02960.12622.49473.3978-3.1618
55.67084.49112.83026.9542.44172.8271-0.0599-0.13260.0242-0.0048-0.018-0.2498-0.13080.04390.04040.10140.02760.01940.1601-0.01040.0901-5.312110.9367-12.6297
61.64651.97360.67455.42261.52860.90120.0654-0.01690.02850.0476-0.10550.30820.0397-0.06920.01640.14710.00010.02740.1658-0.00840.1402-14.14187.4418-9.2725
75.56066.31821.12226.68411.29560.23390.0040.13580.37850.0392-0.03580.6051-0.0676-0.05220.01540.15190.0114-0.0060.1547-0.00860.167-17.579712.3111-19.1333
85.23633.0549-0.42753.5534-0.35421.2679-0.28050.3996-0.515-0.25560.2904-0.4251-0.12730.2426-0.09790.13630.01890.0310.16820.00470.1557-5.582712.7012-20.4937
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 58 through 97 )
2X-RAY DIFFRACTION2chain 'A' and (resid 98 through 121 )
3X-RAY DIFFRACTION3chain 'A' and (resid 122 through 150 )
4X-RAY DIFFRACTION4chain 'A' and (resid 151 through 200 )
5X-RAY DIFFRACTION5chain 'B' and (resid 57 through 87 )
6X-RAY DIFFRACTION6chain 'B' and (resid 88 through 121 )
7X-RAY DIFFRACTION7chain 'B' and (resid 122 through 150 )
8X-RAY DIFFRACTION8chain 'B' and (resid 151 through 198 )

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