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- PDB-8bmv: Ligand binding domain of the P. Putida receptor McpH in complex w... -

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Basic information

Entry
Database: PDB / ID: 8bmv
TitleLigand binding domain of the P. Putida receptor McpH in complex with Uric acid
ComponentsMethyl-accepting chemotaxis protein McpH
KeywordsSIGNALING PROTEIN / LIGAND BINDING DOMAIN / chemoreceptor / PSEUDOMONAS PUTIDA / CHEMOTACTIC TRANSDUCER
Function / homology
Function and homology information


chemotaxis / signal transduction / plasma membrane
Similarity search - Function
Double Cache domain 1 / Cache domain / 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
URIC ACID / Methyl-accepting chemotaxis protein McpH
Similarity search - Component
Biological speciesPseudomonas putida KT2440 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGavira, J.A. / Krell, T. / Fernandez, M. / Martinez-Rodriguez, S.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-112612GB-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-116261GB- I00 Spain
CitationJournal: Nat Commun / Year: 2024
Title: Ubiquitous purine sensor modulates diverse signal transduction pathways in bacteria.
Authors: Monteagudo-Cascales, E. / Gumerov, V.M. / Fernandez, M. / Matilla, M.A. / Gavira, J.A. / Zhulin, I.B. / Krell, T.
History
DepositionNov 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyl-accepting chemotaxis protein McpH
B: Methyl-accepting chemotaxis protein McpH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5674
Polymers61,2312
Non-polymers3362
Water2,090116
1
A: Methyl-accepting chemotaxis protein McpH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7832
Polymers30,6151
Non-polymers1681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyl-accepting chemotaxis protein McpH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7832
Polymers30,6151
Non-polymers1681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.581, 124.322, 57.201
Angle α, β, γ (deg.)90.00, 99.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Methyl-accepting chemotaxis protein McpH


Mass: 30615.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria)
Strain: ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440
Gene: mcpH, PP_0320
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q88R14
#2: Chemical ChemComp-URC / URIC ACID / 7,9-DIHYDRO-1H-PURINE-2,6,8(3H)-TRIONE


Mass: 168.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.83 Å3/Da / Density % sol: 32.7 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 100 mM cacodilato sodico a diferentes pH5.0, 30% Peg 8000,10% Glicerol,20 mM AcNA
PH range: 5.0 - 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.95→124.32 Å / Num. obs: 31404 / % possible obs: 96.1 % / Redundancy: 2.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.039 / Rrim(I) all: 0.068 / Χ2: 1.02 / Net I/σ(I): 11.4 / Num. measured all: 91788
Reflection shellResolution: 1.95→2 Å / % possible obs: 99.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.78 / Num. measured all: 6969 / Num. unique obs: 2283 / CC1/2: 0.602 / Rpim(I) all: 0.532 / Rrim(I) all: 0.948 / Χ2: 0.92 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
Aimlessdata scaling
XDSdata reduction
PHENIX1..20.1-4487refinement
REFMAC5.8.0135refinement
MOLREP11.0 /22.07.2010/phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AF2

Resolution: 1.95→32.15 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 1581 5.04 %
Rwork0.1822 --
obs0.1847 31365 96.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→32.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3854 0 24 116 3994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.005
X-RAY DIFFRACTIONf_dihedral_angle_d5.629596
X-RAY DIFFRACTIONf_chiral_restr0.06606
X-RAY DIFFRACTIONf_plane_restr0.009758
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.010.30261490.26132784X-RAY DIFFRACTION99
2.01-2.080.33581040.27312372X-RAY DIFFRACTION84
2.08-2.170.33021410.23712839X-RAY DIFFRACTION99
2.17-2.270.29881210.2182451X-RAY DIFFRACTION88
2.27-2.390.25771610.20812787X-RAY DIFFRACTION99
2.39-2.540.24391610.20612780X-RAY DIFFRACTION99
2.54-2.730.29561550.21522809X-RAY DIFFRACTION99
2.73-3.010.23251390.19162777X-RAY DIFFRACTION99
3.01-3.440.24161550.18412714X-RAY DIFFRACTION97
3.44-4.330.19491470.15212718X-RAY DIFFRACTION96
4.34-32.150.19431480.15522753X-RAY DIFFRACTION96
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)
11.5902-0.47840.1080.4190.61851.2201-0.04760.00040.2219-0.07290.03750.0752-0.25440.0712-0.00390.2532-0.0098-0.00610.2490.00190.2095-4.6277-0.031134.2748
21.2595-0.230.11071.61560.14781.2939-0.02270.0574-0.004-0.18460.02840.12820.0375-0.18120.00010.2032-0.0273-0.03250.19280.02880.1945-11.0092-16.248627.6591
31.09181.2226-0.07861.25970.18371.1128-0.0542-0.18120.10440.22440.15440.0796-0.1489-0.0528-0.00050.2843-0.00710.00030.22910.03060.2589-9.7996-6.145929.1179
40.2901-0.0584-0.51951.39690.57671.1850.09250.63570.3923-1.73120.12460.1569-0.7411-0.3761-0.0880.8855-0.13230.13390.26650.09420.5045-9.213313.050318.7656
50.48620.348-0.13570.35960.15230.271-0.343-0.12030.3609-0.16820.18590.0969-0.1872-0.19990.00410.624-0.0338-0.04780.2714-0.0020.5246-7.491217.751723.7755
60.5472-0.0701-0.20850.06350.03630.5869-0.1189-0.17090.2892-0.34240.2609-0.1715-0.1338-0.00170.00050.3492-0.0413-0.01380.3726-0.04420.36335.83312.127-14.215
71.20010.7396-0.27581.895-0.11681.56840.0463-0.2053-0.03580.13980.0548-0.0204-0.00120.331900.1862-0.0047-0.00450.3678-0.0020.22486.7902-12.6368-1.0255
80.2358-0.18070.08670.41440.19810.49250.064-0.2385-0.18910.0993-0.1507-0.6052-0.1690.4315-00.243-0.09340.02760.52290.00690.341411.2364-0.1616-5.1461
90.0855-0.146-0.07970.21250.07540.0276-0.22150.08510.53680.0943-0.0148-0.19-0.33350.2514-0.00180.387-0.1814-0.0480.50530.0530.457412.462518.4829-7.1843
100.2412-0.3221-0.35211.5502-0.4171.13060.2542-0.15850.45580.7648-0.43990.5131-0.58020.2853-0.02030.3826-0.17590.04260.3718-0.06910.35486.808821.8155-2.6324
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 129 )
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 164 )
4X-RAY DIFFRACTION4chain 'A' and (resid 165 through 223 )
5X-RAY DIFFRACTION5chain 'A' and (resid 224 through 251 )
6X-RAY DIFFRACTION6chain 'B' and (resid 7 through 40 )
7X-RAY DIFFRACTION7chain 'B' and (resid 41 through 142 )
8X-RAY DIFFRACTION8chain 'B' and (resid 143 through 163 )
9X-RAY DIFFRACTION9chain 'B' and (resid 164 through 176 )
10X-RAY DIFFRACTION10chain 'B' and (resid 177 through 255 )

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