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- PDB-2y0t: The mechanisms of HAMP-mediated signaling in transmembrane recept... -

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Basic information

Entry
Database: PDB / ID: 2y0t
TitleThe mechanisms of HAMP-mediated signaling in transmembrane receptors - the A291F mutant
ComponentsAF1503
KeywordsMEMBRANE PROTEIN / TRANSMEMBRANE SIGNALLING
Function / homology
Function and homology information


histidine kinase / phosphorelay signal transduction system / kinase activity / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
HAMP domain in histidine kinase / : / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsZeth, K. / Ferris, H.U. / Hulko, M. / Lupas, A.N.
CitationJournal: Structure / Year: 2011
Title: The Mechanisms of Hamp-Mediated Signaling in Transmembrane Receptors.
Authors: Ferris, H.U. / Dunin-Horkawicz, S. / Mondejar, L.G. / Hulko, M. / Hantke, K. / Martin, J. / Schultz, J.E. / Zeth, K. / Lupas, A.N. / Coles, M.
History
DepositionDec 7, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references / Version format compliance
Revision 1.2Dec 7, 2016Group: Other / Structure summary
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AF1503
B: AF1503


Theoretical massNumber of molelcules
Total (without water)12,1682
Polymers12,1682
Non-polymers00
Water2,144119
1
A: AF1503
B: AF1503

A: AF1503
B: AF1503


Theoretical massNumber of molelcules
Total (without water)24,3364
Polymers24,3364
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4460 Å2
ΔGint-41.2 kcal/mol
Surface area10340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.070, 34.320, 47.650
Angle α, β, γ (deg.)90.00, 117.79, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A280 - 330
2115B280 - 330

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Components

#1: Protein AF1503


Mass: 6083.946 Da / Num. of mol.: 2 / Fragment: HAMP DOMAIN, RESIDUES 278-331 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Description: GENOMIC DNA / Plasmid: GST-FUSION / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O28769
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ALA 291 TO PHE ENGINEERED RESIDUE IN CHAIN B, ALA 291 TO PHE

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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: 2.62 Å3/Da / Density % sol: 47.86 % / Description: NONE
Crystal growpH: 6.5 / Details: 20 MM MOPS, 100 MM NACL, 20% PEG 3350., pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.976
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.3→20 Å / Num. obs: 28953 / % possible obs: 94.7 % / Observed criterion σ(I): 3.6 / Redundancy: 3.05 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 19.6
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 3.08 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.6 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 1.3→19.56 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.621 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20855 1559 5.1 %RANDOM
Rwork0.17311 ---
obs0.17491 28953 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 22.026 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20.06 Å2
2---0.03 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.3→19.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms796 0 0 119 915
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.022848
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.7621.9831156
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0165115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.5992440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19815171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6051510
X-RAY DIFFRACTIONr_chiral_restr0.2040.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021628
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3491.5530
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.2982871
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.973318
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.0164.5276
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.1483848
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A189medium positional0.470.5
2B189medium positional0.470.5
1A177loose positional1.045
2B177loose positional1.045
1A189medium thermal2.62
2B189medium thermal2.62
1A177loose thermal3.1110
2B177loose thermal3.1110
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 109 -
Rwork0.264 2093 -
obs--96.62 %
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)
11.1797-0.17240.06374.2281-1.7092.0444-0.0780.04520.045-0.01490.0188-0.1703-0.02690.04330.05920.0784-0.01610.00260.05310.00480.04939.921417.271
21.3964-1.09871.41062.2197-0.67282.23430.11920.1526-0.1156-0.1919-0.03740.03930.10310.1645-0.08190.07340.00780.0040.0677-0.00720.03947.453-4.10910.682
33.284-1.28221.028211.01610.77115.5547-0.31250.25650.1569-0.42560.2381-0.2372-0.60790.58890.07440.1643-0.0507-0.01950.10360.01490.01325.0625.611-0.401
41.68330.6281.00541.08380.51042.883-0.0607-0.02130.1995-0.0613-0.06040.1422-0.2329-0.20180.12110.0784-0.0022-0.00290.09160.00450.0717-0.1138.31718.023
53.931-0.11610.37621.90380.34420.72550.0991-0.21210.0459-0.1179-0.23420.2528-0.1841-0.45120.13510.08560.1122-0.00480.2838-0.08260.0827-6.2242.23318.123
62.620.58711.88932.8991.40896.34930.2616-0.2146-0.30680.1534-0.07930.13230.4166-0.2731-0.18230.0628-0.03720.00940.10290.02270.0999-2.602-4.7421.29
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A279 - 298
2X-RAY DIFFRACTION2A299 - 323
3X-RAY DIFFRACTION3A324 - 330
4X-RAY DIFFRACTION4B280 - 296
5X-RAY DIFFRACTION5B297 - 313
6X-RAY DIFFRACTION6B314 - 328

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