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- PDB-2y0q: The mechanisms of HAMP-mediated signaling in transmembrane recept... -

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Basic information

Entry
Database: PDB / ID: 2y0q
TitleThe mechanisms of HAMP-mediated signaling in transmembrane receptors - the A291C mutant
ComponentsUNCHARACTERIZED PROTEIN
KeywordsMEMBRANE PROTEIN / TRANSMEMBRANE SIGNALLING
Function / homology
Function and homology information


signal transduction / membrane / identical protein binding / metal ion binding
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
HAMP domain-containing protein
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.2May 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: UNCHARACTERIZED PROTEIN
B: UNCHARACTERIZED PROTEIN
C: UNCHARACTERIZED PROTEIN
D: UNCHARACTERIZED PROTEIN


Theoretical massNumber of molelcules
Total (without water)24,1604
Polymers24,1604
Non-polymers00
Water2,252125
1
A: UNCHARACTERIZED PROTEIN
B: UNCHARACTERIZED PROTEIN


Theoretical massNumber of molelcules
Total (without water)12,0802
Polymers12,0802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-20 kcal/mol
Surface area5390 Å2
MethodPISA
2
C: UNCHARACTERIZED PROTEIN
D: UNCHARACTERIZED PROTEIN


Theoretical massNumber of molelcules
Total (without water)12,0802
Polymers12,0802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-16.8 kcal/mol
Surface area5810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.190, 55.450, 158.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A3 - 50
2114B3 - 50
1124C3 - 50
2124D3 - 50

NCS ensembles :
ID
1
2

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Components

#1: Protein
UNCHARACTERIZED PROTEIN / AF1503


Mass: 6039.916 Da / Num. of mol.: 4 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ALA 291 TO CYS ENGINEERED RESIDUE IN CHAIN B, ALA 291 TO CYS ...ENGINEERED RESIDUE IN CHAIN A, ALA 291 TO CYS ENGINEERED RESIDUE IN CHAIN B, ALA 291 TO CYS ENGINEERED RESIDUE IN CHAIN C, ALA 291 TO CYS ENGINEERED RESIDUE IN CHAIN D, ALA 291 TO CYS

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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: 1.84 Å3/Da / Density % sol: 32.74 % / Description: NONE
Crystal growpH: 5.6 / Details: pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→2.05 Å / Num. obs: 10902 / % possible obs: 97.2 % / Observed criterion σ(I): 2.1 / Redundancy: 4.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.3
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.1 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.898 / SU B: 12.84 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.285 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26939 573 5 %RANDOM
Rwork0.21541 ---
obs0.21818 10902 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.675 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.99 Å20 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1575 0 0 125 1700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221601
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.9922158
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4985205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.03923.88972
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.44515323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6461520
X-RAY DIFFRACTIONr_chiral_restr0.0910.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211156
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_it0.511.51020
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.90621655
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5163581
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5194.5500
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A369medium positional0.40.5
12B369medium positional0.40.5
21C360medium positional0.480.5
22D360medium positional0.480.5
11A369medium thermal0.562
12B369medium thermal0.562
21C360medium thermal0.642
22D360medium thermal0.642
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 41 -
Rwork0.195 795 -
obs--100 %
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)
119.8506-5.84032.82177.0378-0.17130.48970.07610.3170.4118-0.0214-0.0886-0.3482-0.01470.05980.01250.2873-0.01530.00450.1087-0.01780.091914.8525.411-3.705
22.26940.1453-0.13281.37330.57972.25260.0284-0.11490.07750.0102-0.0099-0.0495-0.25130.0409-0.01850.17870.0297-0.0130.0537-0.00940.09817.82511.532-8.784
327.2227-5.20512.52378.7304-2.46797.70551.57360.80430.1201-0.3006-0.45490.4602-0.497-0.4425-1.11860.25320.13420.11630.11680.03920.2454-3.87114.863-11.844
410.5928-5.8534-1.25326.6111-4.02316.7575-0.2346-0.0581-0.42340.196-0.1986-0.0288-0.02650.36540.43320.1550.0868-0.02670.08180.02250.191116.488-3.937-15.063
51.4478-0.6738-0.48012.9635-1.19730.95590.08380.2723-0.1199-0.1072-0.10790.10330.047-0.12470.02420.14240.0416-0.00320.098-0.03110.11853.0040.371-15.883
65.6219-3.07431.57622.9737-1.49912.6762-0.06870.0258-0.07250.1481-0.05650.14180.0981-0.35640.12530.13150.01210.01560.1129-0.01880.12052.2240.118-7.185
71.7834-0.5647-0.49194.078-1.47991.5101-0.07170.3763-0.0989-0.2050.02410.0292-0.0101-0.18870.04770.1015-0.0091-0.02060.2817-0.01710.04259.09110.94-36.242
82.0273-3.5786-0.230510.6406-1.74861.92220.02230.0932-0.11320.2846-0.05010.1271-0.02620.08960.02770.0989-0.00120.00940.18770.01010.05859.0527.239-26.06
918.2606-3.97654.392830.43975.98582.7125-0.3061-0.07440.21820.7471-0.23322.16990.1034-0.07570.53930.2050.09220.00660.3686-0.02990.20151.32919.942-29.046
1011.87010.33566.057516.3699-1.9393.37560.16830.5492-0.6223-0.12660.0674-0.48160.10650.278-0.23560.05130.02970.04280.228-0.05870.125921.5984.59-23.478
113.0573-0.8433-0.95753.52730.34790.40420.01590.02010.10070.1129-0.0635-0.132-0.01960.02490.04760.0693-0.0025-0.0130.258-0.00910.077119.41516.251-28.09
1222.55842.61397.025122.854-6.88484.8307-0.58480.280.5850.00390.47960.2468-0.1975-0.05290.10510.09190.0231-0.00620.3321-0.01880.032114.72128.123-31.335
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A280 - 289
2X-RAY DIFFRACTION2A290 - 313
3X-RAY DIFFRACTION3A314 - 329
4X-RAY DIFFRACTION4B278 - 283
5X-RAY DIFFRACTION5B284 - 307
6X-RAY DIFFRACTION6B308 - 329
7X-RAY DIFFRACTION7C281 - 306
8X-RAY DIFFRACTION8C307 - 322
9X-RAY DIFFRACTION9C323 - 328
10X-RAY DIFFRACTION10D278 - 285
11X-RAY DIFFRACTION11D286 - 322
12X-RAY DIFFRACTION12D323 - 330

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