PDB-3zrw: The structure of the dimeric Hamp-Dhp fusion A291V mutant

ID or keywords:

Entry

Database: PDB / ID: 3zrw

Title

The structure of the dimeric Hamp-Dhp fusion A291V mutant

Components

(AF1503 PROTEIN, OSMOLARITY SENSOR PROTEIN ENVZ) x 2

Keywords

SIGNALING PROTEIN / OSMOREGULATION / OMPR / OMPC

Function / homology

Function and homology information

response to osmotic stress / histidine kinase / phosphorelay signal transduction system / phosphoprotein phosphatase activity / phosphorelay sensor kinase activity / outer membrane-bounded periplasmic space / protein autophosphorylation / phosphorylation / signal transduction / protein homodimerization activity ...
Similarity search - Function

Biological species

ARCHAEOGLOBUS FULGIDUS (archaea)

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

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

Citation

Journal: Structure / Year: 2012
Title: Mechanism of Regulation of Receptor Histidine Kinases.
Authors: Ferris, H.U. / Dunin-Horkwicz, S. / Hornig, N. / Hulko, M. / Martin, J. / Schultz, J.E. / Zeth, K. / Lupas, A.N. / Coles, M.

History

Deposition	Jun 20, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 29, 2011	Provider: repository / Type: Initial release
Revision 1.1	Apr 25, 2012	Group: Database references / Version format compliance
Revision 1.2	Mar 15, 2017	Group: Source and taxonomy
Revision 1.3	Dec 20, 2023	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 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3zrw.cif.gz	192.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3zrw.ent.gz	156.7 KB	Display	PDB format
PDBx/mmJSON format	3zrw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3zrw_validation.pdf.gz	454.6 KB	Display	wwPDB validaton report
Full document	3zrw_full_validation.pdf.gz	468.8 KB	Display
Data in XML	3zrw_validation.xml.gz	21.5 KB	Display
Data in CIF	3zrw_validation.cif.gz	30.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zr/3zrw ftp://data.pdbj.org/pub/pdb/validation_reports/zr/3zrw	HTTPS FTP

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Related structure data

Related structure data	2lfrC 2lfsC 3zrvC 3zrxC 2asmS 2y0q 2y0t 2y20 2y21 C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3j6n-d 3jz7-d 6tpu-2 4yfe-2 2lfs-d 4fs0-d 1dr9-d 2lfr-d 4uid-1 6tpu-1 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#190 - Oct 2015 Two-component Systems similarity (12) #183 - Mar 2015 Phototropin similarity (8) #158 - Feb 2013 Proton-Gated Urea Channel similarity (4)

Deposited unit

A: AF1503 PROTEIN, OSMOLARITY SENSOR PROTEIN ENVZ

B: AF1503 PROTEIN, OSMOLARITY SENSOR PROTEIN ENVZ

C: AF1503 PROTEIN, OSMOLARITY SENSOR PROTEIN ENVZ

D: AF1503 PROTEIN, OSMOLARITY SENSOR PROTEIN ENVZ

52.6 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: AF1503 PROTEIN, OSMOLARITY SENSOR PROTEIN ENVZ

B: AF1503 PROTEIN, OSMOLARITY SENSOR PROTEIN ENVZ

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

2

C: AF1503 PROTEIN, OSMOLARITY SENSOR PROTEIN ENVZ

D: AF1503 PROTEIN, OSMOLARITY SENSOR PROTEIN ENVZ

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

Unit cell

Length a, b, c (Å)	70.860, 46.670, 157.460
Angle α, β, γ (deg.)	90.00, 94.31, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	C
2	2	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	3	A	3 - 108
2	1	1	3	B	3 - 108
1	1	2	3	C	3 - 108
2	1	2	3	D	3 - 108

NCS ensembles :

ID
1
2

#1: Protein	AF1503 PROTEIN, OSMOLARITY SENSOR PROTEIN ENVZ / HAMP-DHP FUSION PROTEIN Mass: 13136.903 Da / Num. of mol.: 3 / Fragment: RESIDUES 278-326,228-288 / Mutation: YES Source method: isolated from a genetically manipulated source Details: CHIMERIC PROTEIN, RESIDUES OF THE PROTEIN AF1503 FROM A. FULGIDUS AND THE OSMOLARITY SENSING PROTEIN FROM E. COLI -ONE MUTATION IN POSITION A291V IS INTRODUCED Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea), (gene. exp.) ESCHERICHIA COLI (E. coli) Strain: DSM 4304, K-12 / Description: PCR FROM E. COLI WT DNA AND A. FULGIDUS WT DNA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O28769, UniProt: P0AEJ4, histidine kinase
#2: Protein	AF1503 PROTEIN, OSMOLARITY SENSOR PROTEIN ENVZ / HAMP-DHP FUSION PROTEIN Mass: 13151.875 Da / Num. of mol.: 1 / Fragment: RESIDUES 278-326,228-288 / Mutation: YES Source method: isolated from a genetically manipulated source Details: CHIMERIC PROTEIN, RESIDUES OF THE PROTEIN AF1503 FROM A. FULGIDUS AND THE OSMOLARITY SENSING PROTEIN FROM E. COLI -ONE MUTATION IN POSITION A291V IS INTRODUCED Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea), (gene. exp.) ESCHERICHIA COLI (E. coli) Strain: DSM 4304, K-12 / Description: PCR FROM E. COLI WT DNA AND A. FULGIDUS WT DNA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O28769, UniProt: P0AEJ4, histidine kinase
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 226 / 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
Sequence details	O28769 AND P0AEJ4 DOMAINS ARE FUSED BY CLONING.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.47 Å³/Da / Density % sol: 50.2 % / Description: NONE
Crystal grow	pH: 7 / Details: 0.4 M MAGNESIUM FORMATE, 0.1 M BIS/TRIS, PH 7.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.979
Detector	Type: MARRESEARCH MX-225 / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.25→20 Å / Num. obs: 23404 / % possible obs: 99.7 % / Observed criterion σ(I): 2.6 / Redundancy: 3.7 % / R_merge(I) obs: 0.09 / Net I/σ(I): 12
Reflection shell	Resolution: 2.25→2.3 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.53 / Mean I/σ(I) obs: 2.6 / % possible all: 99.7

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ASM

2asm

Resolution: 2.25→25 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.899 / SU B: 16.245 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.322 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26946	1264	5.1 %	RANDOM
R_work	0.21414	-	-	-
obs	0.21696	23404	99.8 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 42.216 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.85 Å²	0 Å²	1.39 Å²
2-	-	-0.46 Å²	0 Å²
3-	-	-	-1.18 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3472	0	0	226	3698

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.022	3505
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.985	1.986	4731
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.517	5	440
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.148	24.678	171
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.284	15	681
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.314	15	36
X-RAY DIFFRACTION	r_chiral_restr	0.117	0.2	569
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	2580
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	0.678	1.5	2205
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.357	2	3567
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.626	3	1300
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	4.814	4.5	1163
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

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	418	tight positional	0.22	0.05
1	2	B	418	tight positional	0.22	0.05
2	1	C	423	tight positional	0.17	0.05
2	2	D	423	tight positional	0.17	0.05
1	1	A	395	loose positional	0.27	5
1	2	B	395	loose positional	0.27	5
2	1	C	399	loose positional	0.3	5
2	2	D	399	loose positional	0.3	5
1	1	A	418	tight thermal	0.16	0.5
1	2	B	418	tight thermal	0.16	0.5
2	1	C	423	tight thermal	0.16	0.5
2	2	D	423	tight thermal	0.16	0.5
1	1	A	395	loose thermal	0.24	10
1	2	B	395	loose thermal	0.24	10
2	1	C	399	loose thermal	0.26	10
2	2	D	399	loose thermal	0.26	10

LS refinement shell

Resolution: 2.25→2.308 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.308	92	-
R_work	0.264	1690	-
obs	-	-	99.83 %

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	13.3677	-0.3142	-0.3696	5.9981	-2.4321	10.3284	0.036	0.6356	-0.1314	-0.5441	-0.1612	-0.3552	0.2083	0.1502	0.1252	0.2842	-0.0671	0.0003	0.3513	0.0343	0.0584	41.622	42.879	7.442
2	23.8847	29.3789	-19.7683	36.6174	-24.8304	16.9544	-0.2282	-0.2201	-0.8472	-0.1117	-0.3121	-0.828	-0.0439	0.3582	0.5403	0.2173	-0.0644	-0.0364	0.4492	0.1005	0.2457	31.666	27.419	23.625
3	1.194	-0.1199	1.036	4.5962	0.803	5.5118	0.1216	0.2616	-0.4067	-0.2741	-0.3272	0.453	0.1895	-0.6702	0.2056	0.2079	0.0473	-0.0658	0.3649	-0.0926	0.3364	6.175	6.491	38.982
4	5.4287	5.4242	-5.1205	8.3934	-8.0569	10.3223	-0.0753	0.8046	-0.0848	-0.4734	0.0313	0.0259	0.3686	0.4593	0.044	0.3137	0.1399	-0.0765	0.6947	0.0379	0.2536	11.359	19.199	27.258
5	6.9253	1.069	0.3067	11.8458	-8.0684	15.6364	-0.0776	-0.1724	0.5124	0.4374	0.2048	-0.456	-1.597	0.0209	-0.1272	0.3621	-0.0778	-0.0126	0.3046	0.0914	0.1893	36.659	53.06	14.377
6	27.8318	26.2951	-21.3468	27.232	-23.0933	19.967	0.14	0.3673	0.7475	0.387	0.3757	0.7291	-0.4367	-0.2186	-0.5156	0.3168	-0.0627	-0.0771	0.6733	0.2421	0.2462	19.418	37.16	23.622
7	4.7442	-2.2793	-0.4596	6.7385	-3.9464	6.5722	-0.0273	0.203	-0.0195	0.4774	0.176	0.3501	-0.4967	-0.5086	-0.1487	0.1578	0.0905	-0.0316	0.2644	-0.0133	0.2728	4.684	13.484	45.019
8	11.5082	12.8111	-8.2775	15.7922	-11.4585	9.5184	0.0409	0.2104	0.5349	0.3522	0.0096	0.3814	-0.3478	0.1225	-0.0504	0.1915	0.061	-0.0673	0.2542	0.0472	0.2931	17.693	19.956	39.971
9	4.5641	3.1002	-3.6379	6.3194	-8.4474	17.3144	0.4321	-0.4962	0.2309	0.1583	0.14	-0.2187	-0.802	0.3296	-0.5721	0.3191	-0.1078	0.0365	0.2074	-0.1053	0.3561	10.11	50.293	100.69
10	1.6732	0.1042	-1.6514	1.802	-0.9513	5.2124	0.227	-0.137	-0.0127	-0.1896	-0.0653	-0.2562	0.0357	0.2484	-0.1618	0.2634	-0.0328	0.0419	0.1446	-0.0168	0.2927	12.036	42.184	93.273
11	4.0399	0.7726	-10.3841	1.1267	-2.5726	27.0889	-0.0204	-0.2368	-0.0629	0.1275	-0.1534	0.0156	0.1368	0.7452	0.1738	0.331	0.0547	0.0166	0.224	0.0263	0.3399	24.52	42.633	63.573
12	1.2395	-0.6133	-1.4486	2.0838	1.0901	4.9378	-0.0473	0.1946	0.1012	0.1247	-0.0913	-0.0772	0.0276	0.2516	0.1386	0.2024	0.0773	-0.0432	0.2302	0.0491	0.2794	25.249	52.14	50.556
13	2.699	-1.3692	-4.6938	4.0155	1.1315	14.5763	0.0186	0.0153	-0.1425	-0.0703	-0.0227	0.3951	0.2044	-0.5492	0.0041	0.242	-0.0645	-0.0082	0.1734	-0.0162	0.3165	-1.649	43.638	95.318
14	2.5359	-0.9226	-0.8003	7.9247	5.9165	9.6253	0.1617	0.197	0.2738	-0.341	-0.2493	0.5494	-0.4803	-0.581	0.0875	0.3106	-0.0562	0.0193	0.1664	0.0223	0.272	-1.257	50.367	90.906
15	1.1829	-0.1159	-4.7338	0.0123	0.4755	19.524	0.0628	0.0478	0.0744	0.0034	-0.0157	-0.0057	0.1706	-0.2245	-0.0471	0.4298	0.0021	0.0428	0.1419	-0.0114	0.308	7.228	52.686	77.012
16	0.4889	0.2623	-1.3084	2.744	-2.5186	5.4308	-0.1209	0.2083	-0.1895	-0.1098	-0.0961	0.1035	0.6162	-0.1957	0.217	0.2714	0.0582	-0.0024	0.246	-0.0264	0.3278	19.628	43.215	47.885

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	278 - 315
2	X-RAY DIFFRACTION	2	A	316 - 347
3	X-RAY DIFFRACTION	3	A	348 - 365
4	X-RAY DIFFRACTION	4	A	366 - 388
5	X-RAY DIFFRACTION	5	B	278 - 318
6	X-RAY DIFFRACTION	6	B	319 - 347
7	X-RAY DIFFRACTION	7	B	348 - 364
8	X-RAY DIFFRACTION	8	B	365 - 387
9	X-RAY DIFFRACTION	9	C	278 - 293
10	X-RAY DIFFRACTION	10	C	294 - 326
11	X-RAY DIFFRACTION	11	C	327 - 353
12	X-RAY DIFFRACTION	12	C	354 - 388
13	X-RAY DIFFRACTION	13	D	278 - 294
14	X-RAY DIFFRACTION	14	D	295 - 312
15	X-RAY DIFFRACTION	15	D	313 - 343
16	X-RAY DIFFRACTION	16	D	344 - 387

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Yorodumi