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

ID or keywords:

Entry

Database: PDB / ID: 2y21

Title

The mechanisms of HAMP-mediated signaling in transmembrane receptors - the A291V mutant

Components

HAMP

Keywords

MEMBRANE 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

Biological species

ARCHAEOGLOBUS FULGIDUS (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.45 Å

Authors

Zeth, K. / Ferris, H.U. / Hulko, M. / Lupas, A.N.

Citation

Journal: 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

Deposition	Dec 12, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 30, 2011	Provider: repository / Type: Initial release
Revision 1.1	Nov 16, 2011	Group: Database references / Version format compliance
Revision 1.2	Jun 20, 2018	Group: 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 1.3	May 8, 2024	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2y21.cif.gz	256.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2y21.ent.gz	214.6 KB	Display	PDB format
PDBx/mmJSON format	2y21.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y2/2y21 ftp://data.pdbj.org/pub/pdb/validation_reports/y2/2y21	HTTPS FTP

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Related structure data

Related structure data	2l7hC 2l7iC 2y0qC 2y0tC 2y20C C: citing same article (ref.)
Similar structure data	4ruv-d 4i16-d 6ms1-2 1i7h-3 2m10-d 6esx-2 2kc1-d 1rap-d 2dge-6 5lso-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#190 - Oct 2015 Two-component Systems similarity (5) #158 - Feb 2013 Proton-Gated Urea Channel similarity (4) #183 - Mar 2015 Phototropin similarity (1)

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

75.7 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

K: HAMP

L: HAMP

defined by author&software
12.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

I: HAMP

J: HAMP

defined by author&software
12.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: HAMP

H: HAMP

defined by author&software
12.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

E: HAMP

F: HAMP

defined by author&software
12.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

C: HAMP

D: HAMP

defined by author&software
12.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

A: HAMP

B: HAMP

defined by author&software
12.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I
10	1	J
11	1	K
12	1	L

NCS domain segments:

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

Dom-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	ILE	ILE	GLU	GLU	A	A	280 - 331	5 - 56
2	HIS	HIS	VAL	VAL	B	B	276 - 328	1 - 53
3	ILE	ILE	GLU	GLU	C	C	280 - 331	5 - 56
4	MET	MET	GLU	GLU	D	D	277 - 331	2 - 56
5	SER	SER	GLU	GLU	E	E	278 - 331	3 - 56
6	MET	MET	GLU	GLU	F	F	277 - 331	2 - 56
7	THR	THR	MET	MET	G	G	279 - 330	4 - 55
8	ILE	ILE	ALA	ALA	H	H	280 - 329	5 - 54
9	ILE	ILE	GLU	GLU	I	I	280 - 331	5 - 56
10	HIS	HIS	ALA	ALA	J	J	276 - 329	1 - 54
11	ILE	ILE	VAL	VAL	K	K	280 - 328	5 - 53
12	MET	MET	ALA	ALA	L	L	277 - 329	2 - 54

#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 details	ENGINEERED 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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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

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

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.972
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.972 Å / Relative weight: 1
Reflection	Resolution: 2.45→20 Å / Num. obs: 27272 / % possible obs: 99.8 % / Observed criterion σ(I): 2.3 / Redundancy: 7.2 % / R_merge(I) obs: 0.06 / Net I/σ(I): 18.3
Reflection shell	Resolution: 2.45→2.51 Å / Redundancy: 7.3 % / R_merge(I) obs: 0.55 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0102	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.45→19.95 Å / Cor.coef. F_o:F_c: 0.938 / Cor.coef. F_o:F_c 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.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28872	1326	5 %	RANDOM
R_work	0.2461	-	-	-
obs	0.24821	25189	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 72.956 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.03 Å²	0 Å²	0 Å²
2-	-	0.02 Å²	0 Å²
3-	-	-	-0.05 Å²

Refinement step

Cycle: LAST / Resolution: 2.45→19.95 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4900	0	0	61	4961

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	4936
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.357	1.991	6632
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.367	5	617
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.907	24.018	224
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.436	15	988
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.314	15	60
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	805
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	3560
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.793	1.5	3143
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.709	2	5075
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.4	3	1793
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	6.63	4.5	1556
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

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

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	tight positional	0.14	0.05
2	B	tight positional	0.08	0.05
3	C	tight positional	0.06	0.05
4	D	tight positional	0.06	0.05
5	E	tight positional	0.05	0.05
6	F	tight positional	0.06	0.05
7	G	tight positional	0.05	0.05
8	H	tight positional	0.06	0.05
9	I	tight positional	0.06	0.05
10	J	tight positional	0.06	0.05
11	K	tight positional	0.06	0.05
12	L	tight positional	0.05	0.05
1	A	tight thermal	0.11	0.5
2	B	tight thermal	0.12	0.5
3	C	tight thermal	0.12	0.5
4	D	tight thermal	0.14	0.5
5	E	tight thermal	0.12	0.5
6	F	tight thermal	0.13	0.5
7	G	tight thermal	0.11	0.5
8	H	tight thermal	0.11	0.5
9	I	tight thermal	0.11	0.5
10	J	tight thermal	0.13	0.5
11	K	tight thermal	0.11	0.5
12	L	tight thermal	0.11	0.5

LS refinement shell

Resolution: 2.45→2.513 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.323	96	-
R_work	0.334	1813	-
obs	-	-	100 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	6.445	2.7963	-1.3536	6.16	0.8329	6.3229	-0.0213	0.8608	0.4715	-0.229	0.1315	0.452	-0.3791	-0.5383	-0.1102	0.153	0.0102	-0.0266	0.2609	0.0321	0.1966	-9.303	-16.1741	17.2085
2	7.9402	3.7604	-2.8952	7.8932	-0.5108	4.9555	-0.0028	-0.141	-0.5783	0.5265	-0.0563	-0.2577	0.3785	0.396	0.0591	0.1925	-0.0316	-0.0869	0.1353	-0.0422	0.1752	-1.9502	-23.6252	25.0005
3	3.8475	-1.956	0.9165	13.5187	-2.4087	5.1506	-0.0957	-0.2736	0.3135	0.1461	0.1459	-1.1018	-0.2679	0.6947	-0.0502	0.0351	-0.0408	-0.04	0.1589	-0.0801	0.2861	-13.7471	-7.8639	39.5705
4	3.9613	0.1654	-1.73	8.9769	2.0616	3.7131	-0.3336	0.297	-0.1202	-0.5963	0.5106	0.4277	0.0954	-0.2512	-0.1769	0.0841	-0.0633	-0.0589	0.1383	0.04	0.1247	-25.6539	-11.2067	35.6198
5	8.076	-3.4123	-0.2644	9.9282	-2.4605	5.0262	0.0305	-0.4627	0.52	0.8831	0.0457	-0.5598	-0.7794	0.5522	-0.0762	0.2028	-0.0134	-0.0323	0.1714	-0.0757	0.113	-7.4024	-10.2052	76.1618
6	5.2965	-2.4446	-0.5402	11.5893	-0.185	3.3329	-0.3516	0.3447	-0.3395	-0.6574	0.2278	0.6041	0.397	-0.3417	0.1238	0.1696	-0.0126	-0.0341	0.1824	-0.027	0.1198	-14.0806	-19.5684	70.6071
7	4.2434	-0.0332	-3.7639	15.4791	-1.5605	8.7101	-0.279	-0.9283	0.1201	0.7124	0.5687	-0.9752	-0.4247	0.3711	-0.2897	0.1552	0.1173	-0.094	0.3674	-0.0353	0.229	9.9149	-8.9038	58.5017
8	4.8746	0.4395	-1.3071	6.8691	-1.0767	5.2815	-0.1275	0.1921	0.035	-0.0964	0.514	0.41	-0.205	-0.8387	-0.3866	0.0252	0.0208	-0.0224	0.4219	0.1291	0.1913	-1.592	-9.2343	52.4589
9	3.2821	0.3387	-1.6162	4.7257	1.6284	3.9034	0.6256	0.1465	0.4689	-0.7313	-0.3737	-0.0045	-0.7979	-0.3792	-0.252	0.5724	-0.0186	0.1119	0.101	0.0315	0.2176	-23.4711	17.3639	9.6092
10	5.7327	3.0776	-1.2215	11.2763	1.0616	3.7676	0.2961	-0.4551	0.2786	0.2545	0.1069	-0.7661	-0.1255	0.6501	-0.403	0.2948	-0.1389	-0.0399	0.1742	-0.0453	0.1587	-16.1968	7.8329	14.4251
11	5.5852	-3.9909	-0.5873	6.9339	3.4203	6.8355	0.4433	0.8056	0.3334	-1.4398	-0.3373	-0.194	-1.3764	0.1978	-0.106	0.6649	0.0565	0.0093	0.1609	0.0222	0.1025	-17.9924	0.9946	-9.3066
12	9.9414	0.2737	-2.3344	7.7942	4.9181	11.3246	0.1347	0.013	-0.8173	0.103	-0.1522	0.0915	0.3745	0.2744	0.0175	0.3253	0.0177	-0.0826	0.043	0.018	0.1428	-18.5644	-9.4071	-1.75

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	280 - 331
2	X-RAY DIFFRACTION	2	B	276 - 331
3	X-RAY DIFFRACTION	3	C	280 - 331
4	X-RAY DIFFRACTION	4	D	277 - 331
5	X-RAY DIFFRACTION	5	E	278 - 331
6	X-RAY DIFFRACTION	6	F	277 - 331
7	X-RAY DIFFRACTION	7	G	279 - 330
8	X-RAY DIFFRACTION	8	H	280 - 329
9	X-RAY DIFFRACTION	9	I	280 - 331
10	X-RAY DIFFRACTION	10	J	276 - 329
11	X-RAY DIFFRACTION	11	K	280 - 328
12	X-RAY DIFFRACTION	12	L	277 - 329

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