PDB-3tmb: Bd1817, a HDG"Y"P protein from Bdellovibrio bacteriovorus

ID or keywords:

Entry

Database: PDB / ID: 3tmb

Title

Bd1817, a HDG"Y"P protein from Bdellovibrio bacteriovorus

Components

Uncharacterized protein Bd1817

Keywords

HYDROLASE / SIGNALING PROTEIN / HD-GYP / phosphodiesterase / UNKNOWN FUNCTION

Function / homology

Function and homology information

metal ion binding
Similarity search - Function

Biological species

Bdellovibrio bacteriovorus (bacteria)

Method

X-RAY DIFFRACTION /

SAD / Resolution: 1.7 Å

Authors

Lovering, A.L.

Citation

Journal: MBio / Year: 2011
Title: The structure of an unconventional HD-GYP protein from Bdellovibrio reveals the roles of conserved residues in this class of cyclic-di-GMP phosphodiesterases.
Authors: Lovering, A.L. / Capeness, M.J. / Lambert, C. / Hobley, L. / Sockett, R.E.

History

Deposition	Aug 31, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 19, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jun 19, 2013	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3tmb.cif.gz	266.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3tmb.ent.gz	216.4 KB	Display	PDB format
PDBx/mmJSON format	3tmb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3tmb_validation.pdf.gz	452.8 KB	Display	wwPDB validaton report
Full document	3tmb_full_validation.pdf.gz	460.7 KB	Display
Data in XML	3tmb_validation.xml.gz	26.9 KB	Display
Data in CIF	3tmb_validation.cif.gz	38.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tm/3tmb ftp://data.pdbj.org/pub/pdb/validation_reports/tm/3tmb	HTTPS FTP

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Related structure data

Related structure data	3tm8C 3tmcC 3tmdC C: citing same article (ref.)
Similar structure data	4a07-d 5t1t-2 5uis-3 6mom-3 6lxy-3 6rfi-1 5lvo-d 5yva-d 2oic-2 4ztn-3 5uit-2 6ti8-1 3tm8-1 4ztl-1 5w84-1 5yvc-d 5vil-2 5k75-4 3qqu-4 5t1s-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

Related structure data

3tm8C

3tmcC

3tmdC

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	#152 - Aug 2012 cAMP-dependent Protein Kinase similarity (2)

Deposited unit

A: Uncharacterized protein Bd1817

B: Uncharacterized protein Bd1817

hetero molecules

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

1

A: Uncharacterized protein Bd1817

hetero molecules

defined by author&software
37.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Uncharacterized protein Bd1817

hetero molecules

defined by author&software
37.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	83.168, 45.451, 98.005
Angle α, β, γ (deg.)	90.00, 113.29, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Uncharacterized protein Bd1817 Mass: 37013.918 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bdellovibrio bacteriovorus (bacteria) / Strain: HD100 / Gene: Bd1817 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6MM30
#2: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.48 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1M Bis Tris pH 5.5, 0.2M Ammonium acetate, 25% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
Detector	Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 1, 2011
Radiation	Monochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 1.7→37.3 Å / Num. all: 72978 / Num. obs: 72760 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.1 % / R_merge(I) obs: 0.053 / Net I/σ(I): 25
Reflection shell	Resolution: 1.7→1.79 Å / % possible all: 85.4

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Processing

Software

Name	Version	Classification
CrystalClear		data collection
PHENIX		model building
PHENIX	(phenix.refine: 1.6.4_486)	refinement
MOSFLM		data reduction
SCALA		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.7→37.292 Å / SU ML: 0.24 / σ(F): 1.08 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2194	6992	5.02 %	random
R_work	0.1935	-	-	-
all	0.1949	72978	-	-
obs	0.1949	139416	96.17 %	-

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 33.038 Å² / k_sol: 0.359 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.3911 Å²	-0 Å²	-1.5094 Å²
2-	-	0.3718 Å²	0 Å²
3-	-	-	-5.7629 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→37.292 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4958	0	14	316	5288

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5099
X-RAY DIFFRACTION	f_angle_d	0.995	6896
X-RAY DIFFRACTION	f_dihedral_angle_d	12.93	1957
X-RAY DIFFRACTION	f_chiral_restr	0.067	774
X-RAY DIFFRACTION	f_plane_restr	0.004	899

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 (%)
1.7004-1.7197	0.344	134	0.3017	2904	X-RAY DIFFRACTION	63
1.7197-1.7399	0.3545	158	0.2999	3419	X-RAY DIFFRACTION	74
1.7399-1.7611	0.2689	205	0.2723	3733	X-RAY DIFFRACTION	81
1.7611-1.7834	0.2861	207	0.2788	3939	X-RAY DIFFRACTION	86
1.7834-1.8069	0.3201	235	0.2648	4214	X-RAY DIFFRACTION	91
1.8069-1.8316	0.3034	221	0.2538	4311	X-RAY DIFFRACTION	95
1.8316-1.8578	0.2624	213	0.246	4532	X-RAY DIFFRACTION	98
1.8578-1.8855	0.2744	220	0.2247	4640	X-RAY DIFFRACTION	100
1.8855-1.915	0.2625	237	0.2169	4502	X-RAY DIFFRACTION	100
1.915-1.9464	0.2393	219	0.2044	4611	X-RAY DIFFRACTION	100
1.9464-1.98	0.2508	270	0.2062	4652	X-RAY DIFFRACTION	100
1.98-2.016	0.2407	210	0.2034	4559	X-RAY DIFFRACTION	100
2.016-2.0547	0.2078	228	0.1972	4658	X-RAY DIFFRACTION	100
2.0547-2.0967	0.2355	217	0.1934	4539	X-RAY DIFFRACTION	100
2.0967-2.1422	0.2434	257	0.1837	4574	X-RAY DIFFRACTION	100
2.1422-2.1921	0.2098	223	0.1825	4649	X-RAY DIFFRACTION	100
2.1921-2.2469	0.2311	249	0.1895	4563	X-RAY DIFFRACTION	100
2.2469-2.3076	0.2145	244	0.185	4565	X-RAY DIFFRACTION	100
2.3076-2.3755	0.2594	252	0.1788	4604	X-RAY DIFFRACTION	100
2.3755-2.4522	0.1782	252	0.1878	4560	X-RAY DIFFRACTION	100
2.4522-2.5398	0.2242	241	0.1868	4601	X-RAY DIFFRACTION	100
2.5398-2.6415	0.1961	288	0.1979	4540	X-RAY DIFFRACTION	100
2.6415-2.7617	0.2458	237	0.2023	4590	X-RAY DIFFRACTION	100
2.7617-2.9072	0.2148	242	0.2051	4584	X-RAY DIFFRACTION	100
2.9072-3.0893	0.2444	237	0.218	4595	X-RAY DIFFRACTION	100
3.0893-3.3277	0.2128	252	0.2115	4591	X-RAY DIFFRACTION	100
3.3277-3.6623	0.2279	277	0.2067	4532	X-RAY DIFFRACTION	100
3.6623-4.1916	0.1868	288	0.1608	4565	X-RAY DIFFRACTION	100
4.1916-5.2786	0.1723	234	0.1461	4581	X-RAY DIFFRACTION	100
5.2786-37.3009	0.1953	245	0.1717	4517	X-RAY DIFFRACTION	98

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	1.2858	0.1478	0.566	0.9089	0.1088	1.1103	0.1167	-0.0802	-0.2055	-0.3698	-0.0566	-0.064	0.4216	-0.047	-0.1131	0.2906	-0.0226	-0.0393	0.1381	-0.013	0.1835	25.9182	-9.2459	-58.8719
2	2.9907	-0.9541	-0.2951	2.3238	0.9169	0.5339	0.1464	-0.1652	0.5494	-0.6157	0.005	0.0811	-0.2658	-0.1398	-0.073	0.2249	0.0321	-0.0505	0.1437	-0.0357	0.2335	23.6037	-0.1138	-57.5298
3	1.415	-0.0203	0.4374	0.7644	0.3824	1.5672	-0.0274	-0.2259	0.1075	-0.0261	-0.0599	0.0739	0.009	-0.3151	0.0728	0.0743	-0.0112	-0.0057	0.1549	-0.0428	0.1654	30.6914	0.332	-42.2988
4	0.565	-0.229	0.2658	0.3486	-0.4179	0.4771	-0.0186	-0.1043	-0.0978	0.0516	0.0504	0.178	0.0212	-0.2102	0.0078	0.0708	-0.0097	0.0234	0.1436	-0.0198	0.1674	39.7873	-1.3159	-37.0961
5	0.6184	-0.0586	-0.0944	1.8049	-0.4247	0.8659	-0.0034	-0.0722	0.0843	-0.157	-0.0879	-0.0862	0.0339	0.0035	0.011	0.0658	-0.0156	0.0176	0.0853	-0.0015	0.1265	51.7498	0.1062	-43.3295
6	1.1143	-0.4435	-0.1219	0.5456	-0.1931	1.1133	-0.2253	-0.1954	0.0063	0.1301	0.2111	-0.0334	0.5796	-0.1761	0.0173	0.247	-0.044	0.0125	0.1878	0.0565	0.1465	48.7478	-11.5104	-29.4075
7	0.3109	0.746	0.4185	2.0341	1.0634	1.6307	-0.1148	-0.0565	0.0619	-0.0236	-0.1006	0.4008	0.2808	-0.0784	0.1888	0.2	-0.0179	0.0106	0.2023	-0.0324	0.2296	53.5371	-3.0148	-113.249
8	4.7637	0.6342	0.1007	0.0899	-0.0338	1.4764	-0.573	-0.35	0.9633	0.0527	0.1074	0.2322	-0.2163	0.1373	0.3357	0.444	0.0234	0.0145	0.305	-0.1481	0.3946	60.8464	8.3654	-102.8286
9	2.565	-0.0702	-0.4074	0.4204	0.7795	2.7056	-0.0961	-0.413	-0.3044	0.2372	0.056	0.2205	1.1696	-0.1207	0.0748	0.3968	0.0092	0.0119	0.1727	-0.0067	0.1783	60.223	-8.4011	-107.1992
10	0.667	0.0998	-0.5814	0.5438	-0.452	2.5943	0.007	0.3046	-0.0393	-0.1823	-0.0367	-0.0852	0.54	0.3379	0.0089	0.2681	0.1023	-0.0148	0.283	-0.0154	0.1374	66.2067	-7.4851	-93.6413
11	0.9112	1.0758	-0.4407	1.5196	0.2597	2.3134	0.1148	0.1794	0.1601	-0.1417	-0.0743	0.2776	0.2056	-0.1699	-0.0171	0.1516	0.0364	-0.0151	0.1884	-0.012	0.163	57.1114	-1.8785	-82.3469
12	0.7432	-0.6137	-0.0859	0.8665	-0.1872	2.5993	0.0073	-0.0734	0.0028	0.2953	0.0253	0.1127	0.1826	0.016	-0.0373	0.2102	0.0062	0.0161	0.1559	-0.0032	0.1268	59.0621	-2.3913	-74.5709

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 2:51)
2	X-RAY DIFFRACTION	2	(chain A and resid 52:73)
3	X-RAY DIFFRACTION	3	(chain A and resid 74:140)
4	X-RAY DIFFRACTION	4	(chain A and resid 141:175)
5	X-RAY DIFFRACTION	5	(chain A and resid 176:277)
6	X-RAY DIFFRACTION	6	(chain A and resid 278:308)
7	X-RAY DIFFRACTION	7	(chain B and resid -11:39)
8	X-RAY DIFFRACTION	8	(chain B and resid 40:52)
9	X-RAY DIFFRACTION	9	(chain B and resid 53:77)
10	X-RAY DIFFRACTION	10	(chain B and resid 78:140)
11	X-RAY DIFFRACTION	11	(chain B and resid 141:210)
12	X-RAY DIFFRACTION	12	(chain B and resid 211:306)

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