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- PDB-6gcv: Ligand binding domain (LBD) of the p. aeruginosa nitrate receptor McpN -

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Basic information

Entry
Database: PDB / ID: 6gcv
TitleLigand binding domain (LBD) of the p. aeruginosa nitrate receptor McpN
ComponentsChemotaxis transducer
KeywordsSIGNALING PROTEIN / chemotaxis / Pseudomonas aeruginosa / chemoreceptor / nitrate
Function / homology
Function and homology information


membrane => GO:0016020 / signal transduction
Similarity search - Function
NarX-like, N-terminal / Type IV pili methyl-accepting chemotaxis transducer N-term / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology 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 profile. / HAMP domain
Similarity search - Domain/homology
ACETATE ION / NITRATE ION / Chemotaxis transducer / Probable chemotaxis transducer
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.3 Å
AuthorsGavira, J.A. / Krell, T. / Martin-Mora, D. / Ortega, A.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2013-4297-P Spain
Spanish Ministry of Economy and CompetitivenessBIO2016-74875-P Spain
CitationJournal: MBio / Year: 2019
Title: The Molecular Mechanism of Nitrate Chemotaxis via Direct Ligand Binding to the PilJ Domain of McpN.
Authors: Martin-Mora, D. / Ortega, A. / Matilla, M.A. / Martinez-Rodriguez, S. / Gavira, J.A. / Krell, T.
History
DepositionApr 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chemotaxis transducer
B: Chemotaxis transducer
C: Chemotaxis transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,01314
Polymers47,5023
Non-polymers51111
Water7,728429
1
A: Chemotaxis transducer
B: Chemotaxis transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,03510
Polymers31,6682
Non-polymers3678
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-39 kcal/mol
Surface area11230 Å2
MethodPISA
2
C: Chemotaxis transducer
hetero molecules

C: Chemotaxis transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9568
Polymers31,6682
Non-polymers2886
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area3520 Å2
ΔGint-22 kcal/mol
Surface area11130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.777, 87.949, 52.896
Angle α, β, γ (deg.)90.00, 93.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-200-

NO3

21C-200-

NO3

31A-361-

HOH

41A-405-

HOH

51B-407-

HOH

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Components

#1: Protein Chemotaxis transducer / Methyl-accepting chemotaxis protein PctC


Mass: 15833.935 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: pctC_5, pctC_1, AOY09_04118, CAZ03_12680, CAZ10_05855, PAMH19_2341, RW109_RW109_03190
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A069QEB8, UniProt: Q9I055*PLUS
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.66 Å3/Da / Density % sol: 53.7 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 7.5
Details: Capillary counterdiffusion method: C23: 0.82 M K-phosphate, 0.82 M Na-phosphate, 0.1 M Na-Hepes pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 21, 2017 / Details: Toroidal Mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.3→46.32 Å / Num. obs: 88758 / % possible obs: 85.43 % / Redundancy: 2.7 % / Biso Wilson estimate: 17.09 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0316 / Rpim(I) all: 0.023 / Rrim(I) all: 0.039 / Net I/σ(I): 14.98
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.3744 / Mean I/σ(I) obs: 2.38 / Num. unique obs: 9541 / CC1/2: 0.837 / Rpim(I) all: 0.2746 / Rrim(I) all: 0.4657 / % possible all: 92.43

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Processing

Software
NameVersionClassification
PHENIXrefinement
REFMAC5.8.0216refinement
XDSdata reduction
SCALAdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.3→46.32 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.349 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.045
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.15325 4375 4.9 %RANDOM
Rwork0.12535 ---
obs0.12673 84383 85.44 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso mean: 23.273 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å2-0.14 Å2
2--0.11 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.3→46.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2830 0 32 429 3291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193323
X-RAY DIFFRACTIONr_bond_other_d0.0010.023167
X-RAY DIFFRACTIONr_angle_refined_deg1.41.9714538
X-RAY DIFFRACTIONr_angle_other_deg0.79637376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1635473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.28723.642173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43315634
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8661547
X-RAY DIFFRACTIONr_chiral_restr0.0880.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023931
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02688
X-RAY DIFFRACTIONr_mcbond_it1.6422.0571662
X-RAY DIFFRACTIONr_mcbond_other1.6242.0511659
X-RAY DIFFRACTIONr_mcangle_it2.1293.0732104
X-RAY DIFFRACTIONr_mcangle_other2.1293.0762105
X-RAY DIFFRACTIONr_scbond_it1.9842.4231661
X-RAY DIFFRACTIONr_scbond_other1.9842.4241662
X-RAY DIFFRACTIONr_scangle_other2.6083.5122394
X-RAY DIFFRACTIONr_long_range_B_refined3.35926.024169
X-RAY DIFFRACTIONr_long_range_B_other3.28525.874143
X-RAY DIFFRACTIONr_rigid_bond_restr2.11436489
X-RAY DIFFRACTIONr_sphericity_free24.2435259
X-RAY DIFFRACTIONr_sphericity_bonded11.51556591
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 349 -
Rwork0.203 6768 -
obs--92.46 %

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