PDB-8dgd: Crystal Structure of GAF domain-containing protein, from Klebsiel...

ID or keywords:

Entry

Database: PDB / ID: 8dgd

Title

Crystal Structure of GAF domain-containing protein, from Klebsiella pneumoniae

Components

GAF domain-containing protein

Keywords

UNKNOWN FUNCTION / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID

Function / homology

Free Met sulfoxide reductase conserved site / Uncharacterized protein family UPF0067 signature. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / DNA binding / GAF domain-containing protein

Function and homology information

Biological species

Klebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.9 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Delker, S.L. / Weiss, M.J. / Lorimer, D.D. / Edwards, T.E. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 1items

Citation

Journal: to be published
Title: Crystal Structure of GAF domain-containing protein, from Klebsiella pneumoniae
Authors: Seattle Structural Genomics Center for Infectious Disease / Delker, S.L. / Weiss, M.J. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Jun 23, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 1, 2023	Provider: repository / Type: Initial release
Revision 1.1	Mar 13, 2024	Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8dgd.cif.gz	149 KB	Display	PDBx/mmCIF format
PDB format	pdb8dgd.ent.gz	116.3 KB	Display	PDB format
PDBx/mmJSON format	8dgd.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8dgd_validation.pdf.gz	450.9 KB	Display	wwPDB validaton report
Full document	8dgd_full_validation.pdf.gz	453.5 KB	Display
Data in XML	8dgd_validation.xml.gz	17.3 KB	Display
Data in CIF	8dgd_validation.cif.gz	24.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dg/8dgd ftp://data.pdbj.org/pub/pdb/validation_reports/dg/8dgd	HTTPS FTP

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Related structure data

Related structure data	1vhmS S: Starting model for refinement
Similar structure data	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	#183 - Mar 2015 Phototropin similarity (3) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (3)

Deposited unit

A: GAF domain-containing protein

B: GAF domain-containing protein

hetero molecules

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

1

A: GAF domain-containing protein

B: GAF domain-containing protein

hetero molecules

A: GAF domain-containing protein

B: GAF domain-containing protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	70.680, 114.380, 73.890
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-202- ZN

#1: Protein	GAF domain-containing protein Mass: 19656.207 Da / Num. of mol.: 2 / Fragment: KlpnC.00048.a.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria) Strain: HS11286 / Gene: KPHS_33640 / Plasmid: KlpnC.00048.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3GUR8
#2: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 2 / Fragment: KlpnC.00048.a.B1 Source method: isolated from a genetically manipulated source Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.9 Å³/Da / Density % sol: 35.24 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Morpheus B3: 10% w/v PEG 4000, 20% v/v glycerol, 0.03M of each halide (0.3M sodium fluoride, 0.3M sodium bromide, 0.3M sodium iodide),0.1M MES/imidazole pH6.5: 321508B3, cok0-10

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
Detector	Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 15, 2021
Radiation	Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 1.9→50 Å / Num. obs: 23992 / % possible obs: 100 % / Redundancy: 6.92 % / B_iso Wilson estimate: 23.43 Å² / CC_1/2: 0.99 / R_merge(I) obs: 0.059 / Net I/σ(I): 23.49
Reflection shell	Resolution: 1.9→1.95 Å / R_merge(I) obs: 0.556 / Mean I/σ(I) obs: 3.92 / Num. unique obs: 1754 / CC_1/2: 0.902

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
SCALEPACK		data scaling
MOLREP		phasing
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1VHM

1vhm

Resolution: 1.9→46.64 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.8 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2196	1939	8.08 %
R_work	0.1724	-	-
obs	0.1763	23989	99.95 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.9→46.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2506	0	2	256	2764

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_dihedral_angle_d	13.942	396
X-RAY DIFFRACTION	f_chiral_restr	0.171	410
X-RAY DIFFRACTION	f_plane_restr	0.007	471

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.9-1.95	0.2607	144	0.2094	1550	X-RAY DIFFRACTION	100
1.95-2	0.2779	136	0.2045	1562	X-RAY DIFFRACTION	100
2-2.06	0.2407	127	0.1903	1534	X-RAY DIFFRACTION	100
2.06-2.13	0.2368	124	0.1727	1596	X-RAY DIFFRACTION	100
2.13-2.2	0.2328	143	0.1765	1525	X-RAY DIFFRACTION	100
2.2-2.29	0.2794	118	0.1761	1588	X-RAY DIFFRACTION	100
2.29-2.39	0.2203	143	0.177	1568	X-RAY DIFFRACTION	100
2.39-2.52	0.2094	155	0.1782	1545	X-RAY DIFFRACTION	100
2.52-2.68	0.2538	125	0.1891	1569	X-RAY DIFFRACTION	100
2.68-2.88	0.2194	141	0.1858	1566	X-RAY DIFFRACTION	100
2.88-3.17	0.2425	152	0.184	1575	X-RAY DIFFRACTION	100
3.18-3.63	0.2012	142	0.1531	1588	X-RAY DIFFRACTION	100
3.63-4.58	0.185	169	0.1452	1572	X-RAY DIFFRACTION	100
4.58-46.64	0.2128	120	0.1753	1712	X-RAY DIFFRACTION	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	2.3824	0.2824	0.3652	1.9289	-0.5058	2.4086	-0.0117	0.08	0.1798	0.0208	0.0061	0.0199	-0.1618	-0.1139	0.0046	0.1172	0.0012	0.0039	0.1329	0.0161	0.121	18.6567	-6.0262	13.7944
2	5.7296	3.7995	-2.0315	7.444	-1.2832	1.9593	0.2689	-0.0998	-0.2107	-0.6247	0.1325	2.1961	-0.239	-1.1151	-0.3543	0.5745	0.2641	-0.0796	0.6547	0.0471	0.7746	3.4336	-0.859	14.7142
3	0.9518	-0.2572	-0.1271	5.0947	0.2398	1.6698	-0.0381	0.1265	0.0746	-0.1433	-0.0378	0.067	-0.0419	-0.0311	0.0671	0.0882	0	-0.0183	0.1449	0.0227	0.0928	18.6717	-8.4935	8.2964
4	7.2034	0.5931	3.4286	4.3474	-0.2108	6.1642	-0.0386	-0.6435	0.5086	0.4059	-0.0059	0.381	0.1077	-1.6014	0.1493	0.1918	-0.0175	0.0404	0.4153	0.0336	0.2695	5.359	-17.1572	37.7037
5	6.5407	0.8183	0.1149	3.5427	0.283	4.9196	0.0726	0.0207	0.1417	0.0831	-0.0301	0.3558	0.0261	-0.853	-0.0695	0.1366	-0.0067	0.0192	0.1978	0.0543	0.161	10.7371	-17.3449	25.8677
6	5.2392	-3.0657	-2.6037	6.677	2.3266	6.2771	-0.0023	-0.2612	0.0631	0.0142	-0.0412	0.0898	-0.1015	0.0056	-0.014	0.1379	-0.0237	-0.0221	0.1442	0.0335	0.1587	21.4125	-17.3681	30.2023
7	2.8323	-0.5386	-0.4758	4.0967	0.5331	4.4866	0.1403	-0.0765	-0.1199	-0.0168	-0.2399	-0.4299	0.2157	0.3163	0.1239	0.152	-0.0018	0.0051	0.1797	0.0587	0.1979	28.16	-22.2625	26.394
8	2.8687	0.4116	1.6868	9.0707	6.1095	4.8989	0.0457	-0.7307	0.0684	0.4182	-0.0004	-0.7354	0.133	0.2815	0.0697	0.3311	-0.0609	-0.0381	0.3685	0.0853	0.3103	27.4777	-24.0176	41.209
9	4.4667	1.088	-2.6082	5.0092	-3.8954	5.9443	0.0087	-0.4968	0.4409	-1.2361	0.4986	-0.2448	1.1063	0.1743	-0.4985	0.565	0.0079	-0.069	0.6297	0.1397	0.5251	34.1043	-18.3369	35.0292
10	2.6769	-0.584	-0.1788	6.5038	2.797	6.3418	-0.0298	-0.0454	-0.3875	-0.3381	-0.0365	0.0344	0.4523	-0.104	0.078	0.1752	-0.0279	-0.0118	0.1579	0.0599	0.1723	20.0538	-25.9489	31.8555
11	2.2944	0.634	-0.4074	2.8543	-0.0888	5.5189	0.1712	-0.3586	-0.1456	0.4126	-0.0167	0.0801	0.2959	-0.3076	-0.1083	0.1844	-0.005	0.0274	0.1794	0.0479	0.1702	14.8697	-22.2253	38.7375
12	4.3524	1.2978	-1.8532	4.4972	-1.2857	5.9593	-0.0345	0.368	-0.6717	-0.3403	0.0084	-0.1859	0.6813	-0.2436	0.0238	0.4298	-0.1558	-0.0139	0.3061	-0.042	0.2652	14.1614	-30.4401	17.8331

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -2 through 93 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 94 through 105 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 106 through 164 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 2 through 18 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 19 through 38 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 39 through 51 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 52 through 81 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 82 through 93 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 94 through 105 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 106 through 126 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 127 through 151 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 152 through 162 )

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