PDB-6saw: Chromophore binding domain of bacteriophytochrome linked diguanyl...

ID or keywords:

Entry

Database: PDB / ID: 6saw

Title

Chromophore binding domain of bacteriophytochrome linked diguanylyl cyclase from Idiomarina species A28L (dimeric Pfr-like state).

Components

Diguanylate cyclase (GGDEF) domain-containing protein

Keywords

LYASE / bacteriophytochrome /

biliverdin / activated conformation

Function / homology

Function and homology information

diguanylate cyclase / detection of visible light /

photoreceptor activity / GTP binding / regulation of DNA-templated transcription /

metal ion binding
Similarity search - Function

Biological species

Idiomarina sp. A28L (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 3 Å

Authors

Gourinchas, G. / Winkler, A.

Funding support

Austria, 1items

Citation

Journal: J.Biol.Chem. / Year: 2020
Title: Distinct chromophore-protein environments enable asymmetric activation of a bacteriophytochrome-activated diguanylate cyclase.
Authors: Buhrke, D. / Gourinchas, G. / Muller, M. / Michael, N. / Hildebrandt, P. / Winkler, A.

History

Deposition	Jul 18, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 11, 2019	Provider: repository / Type: Initial release
Revision 1.1	Dec 25, 2019	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Jan 22, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3	Jan 24, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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	6saw.cif.gz	499 KB	Display	PDBx/mmCIF format
PDB format	pdb6saw.ent.gz	412.3 KB	Display	PDB format
PDBx/mmJSON format	6saw.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sa/6saw ftp://data.pdbj.org/pub/pdb/validation_reports/sa/6saw	HTTPS FTP

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Related structure data

Related structure data	6saxC 6et7S 5llw 5lly S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6fv3-2 6fv4-d 6hcl-d 6eo5-d 5jzx-2 6och-d 4psx-1 4psx-2 4rg5-d 1qs0-d 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

S: Starting model for refinement

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	#183 - Mar 2015 Phototropin similarity (12) #251 - Nov 2020 Adenylyl Cyclase similarity (1) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (4) #133 - Jan 2011 Nitric Oxide Synthase similarity (1) #58 - Oct 2004 G Proteins similarity (1)

Deposited unit

A: Diguanylate cyclase (GGDEF) domain-containing protein

B: Diguanylate cyclase (GGDEF) domain-containing protein

C: Diguanylate cyclase (GGDEF) domain-containing protein

D: Diguanylate cyclase (GGDEF) domain-containing protein

E: Diguanylate cyclase (GGDEF) domain-containing protein

F: Diguanylate cyclase (GGDEF) domain-containing protein

G: Diguanylate cyclase (GGDEF) domain-containing protein

H: Diguanylate cyclase (GGDEF) domain-containing protein

hetero molecules

292 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Diguanylate cyclase (GGDEF) domain-containing protein

hetero molecules

C: Diguanylate cyclase (GGDEF) domain-containing protein

hetero molecules

defined by software
Evidence: gel filtration, Based on gel filtration analysis, the main dimer assembly is defined by the non-native dimer interface between the following protomers: A/C B/E D/G F/H
73 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Diguanylate cyclase (GGDEF) domain-containing protein

hetero molecules

E: Diguanylate cyclase (GGDEF) domain-containing protein

hetero molecules

defined by software
Evidence: The native-interface is represented by the following protomer interfaces: A/D B/F E/G C/H
73 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

D: Diguanylate cyclase (GGDEF) domain-containing protein

G: Diguanylate cyclase (GGDEF) domain-containing protein

hetero molecules

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

4

F: Diguanylate cyclase (GGDEF) domain-containing protein

H: Diguanylate cyclase (GGDEF) domain-containing protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	344.650, 344.650, 92.440
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	146
Space group name H-M	H3

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	(chain A and (resid 6 through 192 or resid 194 through 312))
2	1	(chain B and (resid 6 through 192 or resid 194 through 312))
3	1	(chain C and (resid 6 through 192 or resid 194 through 312))
4	1	(chain D and (resid 6 through 192 or resid 194 through 312))
5	1	(chain E and (resid 6 through 192 or resid 194 through 312))
6	1	(chain F and (resid 6 through 192 or resid 194 through 312))
7	1	(chain G and (resid 6 through 192 or resid 194 through 312))
8	1	(chain H and (resid 6 through 192 or resid 194 through 312))

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLY	GLY	ASN	ASN	(chain A and (resid 6 through 192 or resid 194 through 312))	A	A	6 - 192	8 - 194
1	2	HIS	HIS	HIS	HIS	(chain A and (resid 6 through 192 or resid 194 through 312))	A	A	194 - 312	196 - 314
2	1	GLY	GLY	ASN	ASN	(chain B and (resid 6 through 192 or resid 194 through 312))	B	B	6 - 192	8 - 194
2	2	HIS	HIS	HIS	HIS	(chain B and (resid 6 through 192 or resid 194 through 312))	B	B	194 - 312	196 - 314
3	1	GLY	GLY	ASN	ASN	(chain C and (resid 6 through 192 or resid 194 through 312))	C	C	6 - 192	8 - 194
3	2	HIS	HIS	HIS	HIS	(chain C and (resid 6 through 192 or resid 194 through 312))	C	C	194 - 312	196 - 314
4	1	GLY	GLY	ASN	ASN	(chain D and (resid 6 through 192 or resid 194 through 312))	D	D	6 - 192	8 - 194
4	2	HIS	HIS	HIS	HIS	(chain D and (resid 6 through 192 or resid 194 through 312))	D	D	194 - 312	196 - 314
5	1	GLY	GLY	ASN	ASN	(chain E and (resid 6 through 192 or resid 194 through 312))	E	E	6 - 192	8 - 194
5	2	HIS	HIS	HIS	HIS	(chain E and (resid 6 through 192 or resid 194 through 312))	E	E	194 - 312	196 - 314
6	1	GLY	GLY	ASN	ASN	(chain F and (resid 6 through 192 or resid 194 through 312))	F	F	6 - 192	8 - 194
6	2	HIS	HIS	HIS	HIS	(chain F and (resid 6 through 192 or resid 194 through 312))	F	F	194 - 312	196 - 314
7	1	GLY	GLY	ASN	ASN	(chain G and (resid 6 through 192 or resid 194 through 312))	G	G	6 - 192	8 - 194
7	2	HIS	HIS	HIS	HIS	(chain G and (resid 6 through 192 or resid 194 through 312))	G	G	194 - 312	196 - 314
8	1	GLY	GLY	ASN	ASN	(chain H and (resid 6 through 192 or resid 194 through 312))	H	H	6 - 192	8 - 194
8	2	HIS	HIS	HIS	HIS	(chain H and (resid 6 through 192 or resid 194 through 312))	H	H	194 - 312	196 - 314

#1: Protein	Diguanylate cyclase (GGDEF) domain-containing protein Mass: 35899.766 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Idiomarina sp. A28L (bacteria) / Gene: A28LD_0430 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F7RW09
#2: Chemical	ChemComp-LBV / 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid / 2(R),3(E)- PHYTOCHROMOBILIN Mass: 585.670 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃₃H₃₇N₄O₆ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.69 Å³/Da / Density % sol: 66.67 % / Description: plate
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris pH6.5, 20 % PEG 5000 MME

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

PETRA III, DESY

/ Beamline: P11 / Wavelength: 1.0047 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.0047 Å / Relative weight: 1

Reflection

Resolution: 3→55.023 Å / Num. obs: 81556 / % possible obs: 99.5 % / Redundancy: 3.484 % / B_iso Wilson estimate: 53.238 Å² / CC_1/2: 0.956 / R_merge(I) obs: 0.286 / R_rim(I) all: 0.338 / Χ²: 0.888 / Net I/σ(I): 4.94 / Num. measured all: 284153 / Scaling rejects: 2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
3-3.1	3.402	1.392	1.12	25952	7676	7629	0.268	1.656	99.4
3.1-3.2	3.387	1.157	1.45	22764	6766	6721	0.399	1.38	99.3
3.2-3.3	3.556	0.946	1.91	21132	5971	5942	0.532	1.124	99.5
3.3-3.4	3.528	0.772	2.46	18346	5244	5200	0.641	0.919	99.2
3.4-3.6	3.467	0.562	3.27	30567	8881	8817	0.79	0.668	99.3
3.6-4	3.417	0.434	4.35	43636	12838	12769	0.849	0.516	99.5
4-6	3.561	0.202	7.13	86432	24328	24269	0.96	0.238	99.8
6-10	3.497	0.118	9.17	28042	8040	8018	0.986	0.139	99.7
10-20	3.349	0.076	13.22	6470	1938	1932	0.987	0.089	99.7
20-55.023	3.135	0.081	14.21	812	279	259	0.981	0.099	92.8

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	2.8 Å	58.06 Å
Translation	2.8 Å	58.06 Å

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Processing

Software

Name	Version	Classification
PHENIX		refinement
XDS		data reduction
XSCALE		data scaling
PHASER	2.8.1	phasing
PDB_EXTRACT	3.25	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6et7

6et7

Resolution: 3→55.023 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 26.97

	R_factor	Num. reflection	% reflection
R_free	0.2292	4077	5 %
R_work	0.1965	-	-
obs	0.1982	81534	99.49 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 178.93 Å² / B_iso mean: 67.0715 Å² / B_iso min: 33.92 Å²

Refinement step

Cycle: final / Resolution: 3→55.023 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19896	0	352	8	20256
B_iso mean	-	-	67.51	68.45	-
Num. residues	-	-	-	-	2456

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	12220	X-RAY DIFFRACTION	8.43	TORSIONAL
1	2	B	12220	X-RAY DIFFRACTION	8.43	TORSIONAL
1	3	C	12220	X-RAY DIFFRACTION	8.43	TORSIONAL
1	4	D	12220	X-RAY DIFFRACTION	8.43	TORSIONAL
1	5	E	12220	X-RAY DIFFRACTION	8.43	TORSIONAL
1	6	F	12220	X-RAY DIFFRACTION	8.43	TORSIONAL
1	7	G	12220	X-RAY DIFFRACTION	8.43	TORSIONAL
1	8	H	12220	X-RAY DIFFRACTION	8.43	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
3-3.0352	0.4692	140	0.4503	2639	99
3.0352-3.0723	0.4133	142	0.4215	2693	99
3.0723-3.1111	0.4392	140	0.4115	2669	100
3.1111-3.1521	0.4291	139	0.3634	2640	99
3.1521-3.1952	0.3272	143	0.3283	2729	99
3.1952-3.2409	0.3373	137	0.3183	2608	99
3.2409-3.2893	0.3384	141	0.3053	2676	100
3.2893-3.3406	0.325	141	0.3253	2667	99
3.3406-3.3954	0.3632	141	0.3297	2679	99
3.3954-3.454	0.3489	140	0.3041	2665	100
3.454-3.5167	0.3056	139	0.2586	2631	99
3.5167-3.5844	0.2996	142	0.2462	2697	99
3.5844-3.6575	0.2722	141	0.2328	2681	99
3.6575-3.737	0.2615	139	0.2287	2642	99
3.737-3.8239	0.2523	140	0.2214	2670	100
3.8239-3.9196	0.2521	141	0.2028	2668	100
3.9196-4.0255	0.2044	143	0.1871	2711	100
4.0255-4.1439	0.2248	138	0.173	2631	100
4.1439-4.2776	0.1975	141	0.1548	2683	100
4.2776-4.4304	0.1729	142	0.1413	2697	100
4.4304-4.6077	0.1609	141	0.1364	2675	100
4.6077-4.8173	0.1695	141	0.1419	2677	100
4.8173-5.0711	0.1742	140	0.1459	2661	100
5.0711-5.3886	0.1869	142	0.1513	2702	100
5.3886-5.8043	0.2135	141	0.1619	2680	100
5.8043-6.3876	0.2041	141	0.1637	2680	100
6.3876-7.31	0.1887	141	0.159	2664	100
7.31-9.2029	0.1565	141	0.1288	2683	100
9.2029-55.023	0.1533	139	0.1417	2659	99

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