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- PDB-3lnr: Crystal structure of poly-HAMP domains from the P. aeruginosa sol... -

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Basic information

Entry
Database: PDB / ID: 3lnr
TitleCrystal structure of poly-HAMP domains from the P. aeruginosa soluble receptor Aer2
ComponentsAerotaxis transducer Aer2
KeywordsSIGNALING PROTEIN / HAMP domain / poly-HAMP domains
Function / homology
Function and homology information


positive aerotaxis / aerotaxis / chemotaxis / transmembrane signaling receptor activity / signal transduction / identical protein binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1530 / HAMP N-terminal domain 3 / : / : / HAMP N-terminal domain 3 / Methyl-accepting chemotaxis protein McpB, second HAMP domain / Methyl-accepting chemotaxis protein McpB, first HAMP domain / HAMP domain / PAS domain / : ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1530 / HAMP N-terminal domain 3 / : / : / HAMP N-terminal domain 3 / Methyl-accepting chemotaxis protein McpB, second HAMP domain / Methyl-accepting chemotaxis protein McpB, first HAMP domain / HAMP domain / PAS domain / : / 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 profile. / HAMP domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / PAS repeat profile. / PAS domain / PAS domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Methyl-accepting chemotaxis protein McpB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.64 Å
AuthorsAirola, M.V. / Bilwes, A.M. / Crane, B.R.
CitationJournal: Structure / Year: 2010
Title: Structure of concatenated HAMP domains provides a mechanism for signal transduction.
Authors: Airola, M.V. / Watts, K.J. / Bilwes, A.M. / Crane, B.R.
History
DepositionFeb 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aerotaxis transducer Aer2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0904
Polymers18,9831
Non-polymers1063
Water63135
1
A: Aerotaxis transducer Aer2
hetero molecules

A: Aerotaxis transducer Aer2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1798
Polymers37,9672
Non-polymers2136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7540 Å2
ΔGint-96 kcal/mol
Surface area16990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.612, 113.612, 66.241
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Aerotaxis transducer Aer2


Mass: 18983.375 Da / Num. of mol.: 1 / Fragment: residues 1-172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: aer2, PA0176 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I6V6
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 5.63 Å3/Da / Density % sol: 78.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.1 M Lithium sulfate, 15-18% glycerol, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918, 0.97857, 0.97914, 0.95682
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 12, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979181
20.978571
30.979141
40.956821
ReflectionResolution: 2.64→40 Å / Num. all: 13227 / Num. obs: 12446 / % possible obs: 94.1 % / Redundancy: 7.1 % / Rsym value: 0.049 / Net I/σ(I): 38.4
Reflection shellResolution: 2.64→2.69 Å / Mean I/σ(I) obs: 4.5 / Rsym value: 0.411 / % possible all: 99.2

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 3.62 Å / D res low: 50 Å / FOM : 0.61 / Reflection: 4983
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
3 wavelength110.97863.8-7.2
3 wavelength120.97912.2-8.4
3 wavelength130.95683.7-2.8
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.5150.590.9922.023
2Se600.4140.4390.1033.48
3Se600.4480.470.1541.887
4Se600.5080.4120.0560.783
Phasing MAD shell
Resolution (Å)FOM Reflection
12.95-500.64257
8.21-12.950.71424
6.43-8.210.69540
5.45-6.430.66621
4.82-5.450.63687
4.36-4.820.6765
4.02-4.360.55809
3.74-4.020.51880

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Processing

Software
NameVersionClassificationNB
SOLVE2.13phasing
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.64→40 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.271 1285 9.7 %
Rwork0.238 --
obs-12446 94.1 %
Solvent computationBsol: 54.079 Å2
Displacement parametersBiso max: 130.13 Å2 / Biso mean: 74.865 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1--5.405 Å20 Å20 Å2
2---5.405 Å20 Å2
3---10.81 Å2
Refinement stepCycle: LAST / Resolution: 2.64→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1231 0 3 35 1269
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4681.5
X-RAY DIFFRACTIONc_scbond_it2.2812
X-RAY DIFFRACTIONc_mcangle_it2.5722
X-RAY DIFFRACTIONc_scangle_it3.6542.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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