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- PDB-2y21: The mechanisms of HAMP-mediated signaling in transmembrane recept... -

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Basic information

Entry
Database: PDB / ID: 2y21
TitleThe mechanisms of HAMP-mediated signaling in transmembrane receptors - the A291V mutant
ComponentsHAMP
KeywordsMEMBRANE PROTEIN / TRANSMEMBRANE SIGNALLING
Function / homology
Function and homology information


signal transduction / identical protein binding / membrane / 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: 2.45 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 12, 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 1.2Jun 20, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: citation / entity ...citation / entity / pdbx_validate_close_contact / struct_conn
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.pdbx_description
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HAMP
B: HAMP
C: HAMP
D: HAMP
E: HAMP
F: HAMP
G: HAMP
H: HAMP
I: HAMP
J: HAMP
K: HAMP
L: HAMP


Theoretical massNumber of molelcules
Total (without water)75,66312
Polymers75,66312
Non-polymers00
Water1,09961
1
K: HAMP
L: HAMP


Theoretical massNumber of molelcules
Total (without water)12,6102
Polymers12,6102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-15.5 kcal/mol
Surface area5750 Å2
MethodPISA
2
I: HAMP
J: HAMP


Theoretical massNumber of molelcules
Total (without water)12,6102
Polymers12,6102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-15.6 kcal/mol
Surface area6100 Å2
MethodPISA
3
G: HAMP
H: HAMP


Theoretical massNumber of molelcules
Total (without water)12,6102
Polymers12,6102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-15.4 kcal/mol
Surface area5790 Å2
MethodPISA
4
E: HAMP
F: HAMP


Theoretical massNumber of molelcules
Total (without water)12,6102
Polymers12,6102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-15.4 kcal/mol
Surface area6560 Å2
MethodPISA
5
C: HAMP
D: HAMP


Theoretical massNumber of molelcules
Total (without water)12,6102
Polymers12,6102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-15.6 kcal/mol
Surface area6350 Å2
MethodPISA
6
A: HAMP
B: HAMP


Theoretical massNumber of molelcules
Total (without water)12,6102
Polymers12,6102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-14.8 kcal/mol
Surface area6030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.150, 81.780, 206.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ILEILEGLUGLUAA280 - 3315 - 56
2HISHISVALVALBB276 - 3281 - 53
3ILEILEGLUGLUCC280 - 3315 - 56
4METMETGLUGLUDD277 - 3312 - 56
5SERSERGLUGLUEE278 - 3313 - 56
6METMETGLUGLUFF277 - 3312 - 56
7THRTHRMETMETGG279 - 3304 - 55
8ILEILEALAALAHH280 - 3295 - 54
9ILEILEGLUGLUII280 - 3315 - 56
10HISHISALAALAJJ276 - 3291 - 54
11ILEILEVALVALKK280 - 3285 - 53
12METMETALAALALL277 - 3292 - 54

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Components

#1: Protein
HAMP / AF1503


Mass: 6305.246 Da / Num. of mol.: 12 / 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.: 61 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ALA 291 TO VAL ENGINEERED RESIDUE IN CHAIN B, ALA 291 TO VAL ...ENGINEERED RESIDUE IN CHAIN A, ALA 291 TO VAL ENGINEERED RESIDUE IN CHAIN B, ALA 291 TO VAL ENGINEERED RESIDUE IN CHAIN C, ALA 291 TO VAL ENGINEERED RESIDUE IN CHAIN D, ALA 291 TO VAL ENGINEERED RESIDUE IN CHAIN E, ALA 291 TO VAL ENGINEERED RESIDUE IN CHAIN F, ALA 291 TO VAL ENGINEERED RESIDUE IN CHAIN G, ALA 291 TO VAL ENGINEERED RESIDUE IN CHAIN H, ALA 291 TO VAL ENGINEERED RESIDUE IN CHAIN I, ALA 291 TO VAL ENGINEERED RESIDUE IN CHAIN J, ALA 291 TO VAL ENGINEERED RESIDUE IN CHAIN K, ALA 291 TO VAL ENGINEERED RESIDUE IN CHAIN L, ALA 291 TO VAL

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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: 2.05 Å3/Da / Density % sol: 39.94 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.972
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.45→20 Å / Num. obs: 27272 / % possible obs: 99.8 % / Observed criterion σ(I): 2.3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.3
Reflection shellResolution: 2.45→2.51 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→19.95 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / SU B: 27.469 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R: 0.597 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28872 1326 5 %RANDOM
Rwork0.2461 ---
obs0.24821 25189 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 72.956 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.45→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4900 0 0 61 4961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224936
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.9916632
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3675617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.90724.018224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.43615988
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3141560
X-RAY DIFFRACTIONr_chiral_restr0.0970.2805
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213560
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_it0.7931.53143
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.70925075
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.431793
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.634.51556
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

Ens-ID: 1 / Number: 376 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.140.05
2Btight positional0.080.05
3Ctight positional0.060.05
4Dtight positional0.060.05
5Etight positional0.050.05
6Ftight positional0.060.05
7Gtight positional0.050.05
8Htight positional0.060.05
9Itight positional0.060.05
10Jtight positional0.060.05
11Ktight positional0.060.05
12Ltight positional0.050.05
1Atight thermal0.110.5
2Btight thermal0.120.5
3Ctight thermal0.120.5
4Dtight thermal0.140.5
5Etight thermal0.120.5
6Ftight thermal0.130.5
7Gtight thermal0.110.5
8Htight thermal0.110.5
9Itight thermal0.110.5
10Jtight thermal0.130.5
11Ktight thermal0.110.5
12Ltight thermal0.110.5
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 96 -
Rwork0.334 1813 -
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)
16.4452.7963-1.35366.160.83296.3229-0.02130.86080.4715-0.2290.13150.452-0.3791-0.5383-0.11020.1530.0102-0.02660.26090.03210.1966-9.303-16.174117.2085
27.94023.7604-2.89527.8932-0.51084.9555-0.0028-0.141-0.57830.5265-0.0563-0.25770.37850.3960.05910.1925-0.0316-0.08690.1353-0.04220.1752-1.9502-23.625225.0005
33.8475-1.9560.916513.5187-2.40875.1506-0.0957-0.27360.31350.14610.1459-1.1018-0.26790.6947-0.05020.0351-0.0408-0.040.1589-0.08010.2861-13.7471-7.863939.5705
43.96130.1654-1.738.97692.06163.7131-0.33360.297-0.1202-0.59630.51060.42770.0954-0.2512-0.17690.0841-0.0633-0.05890.13830.040.1247-25.6539-11.206735.6198
58.076-3.4123-0.26449.9282-2.46055.02620.0305-0.46270.520.88310.0457-0.5598-0.77940.5522-0.07620.2028-0.0134-0.03230.1714-0.07570.113-7.4024-10.205276.1618
65.2965-2.4446-0.540211.5893-0.1853.3329-0.35160.3447-0.3395-0.65740.22780.60410.397-0.34170.12380.1696-0.0126-0.03410.1824-0.0270.1198-14.0806-19.568470.6071
74.2434-0.0332-3.763915.4791-1.56058.7101-0.279-0.92830.12010.71240.5687-0.9752-0.42470.3711-0.28970.15520.1173-0.0940.3674-0.03530.2299.9149-8.903858.5017
84.87460.4395-1.30716.8691-1.07675.2815-0.12750.19210.035-0.09640.5140.41-0.205-0.8387-0.38660.02520.0208-0.02240.42190.12910.1913-1.592-9.234352.4589
93.28210.3387-1.61624.72571.62843.90340.62560.14650.4689-0.7313-0.3737-0.0045-0.7979-0.3792-0.2520.5724-0.01860.11190.1010.03150.2176-23.471117.36399.6092
105.73273.0776-1.221511.27631.06163.76760.2961-0.45510.27860.25450.1069-0.7661-0.12550.6501-0.4030.2948-0.1389-0.03990.1742-0.04530.1587-16.19687.832914.4251
115.5852-3.9909-0.58736.93393.42036.83550.44330.80560.3334-1.4398-0.3373-0.194-1.37640.1978-0.1060.66490.05650.00930.16090.02220.1025-17.99240.9946-9.3066
129.94140.2737-2.33447.79424.918111.32460.13470.013-0.81730.103-0.15220.09150.37450.27440.01750.32530.0177-0.08260.0430.0180.1428-18.5644-9.4071-1.75
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A280 - 331
2X-RAY DIFFRACTION2B276 - 331
3X-RAY DIFFRACTION3C280 - 331
4X-RAY DIFFRACTION4D277 - 331
5X-RAY DIFFRACTION5E278 - 331
6X-RAY DIFFRACTION6F277 - 331
7X-RAY DIFFRACTION7G279 - 330
8X-RAY DIFFRACTION8H280 - 329
9X-RAY DIFFRACTION9I280 - 331
10X-RAY DIFFRACTION10J276 - 329
11X-RAY DIFFRACTION11K280 - 328
12X-RAY DIFFRACTION12L277 - 329

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