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

ID or keywords:

Entry

Database: PDB / ID: 3tmc

Title

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

Components

Uncharacterized protein

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: 1.55 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_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	3tmc.cif.gz	248.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3tmc.ent.gz	199.2 KB	Display	PDB format
PDBx/mmJSON format	3tmc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3tmc_validation.pdf.gz	457.9 KB	Display	wwPDB validaton report
Full document	3tmc_full_validation.pdf.gz	464 KB	Display
Data in XML	3tmc_validation.xml.gz	26.4 KB	Display
Data in CIF	3tmc_validation.cif.gz	37.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tm/3tmc ftp://data.pdbj.org/pub/pdb/validation_reports/tm/3tmc	HTTPS FTP

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Related structure data

Related structure data	3tm8C 3tmbC 3tmdC C: citing same article (ref.)
Similar structure data	6yrc-6 2f5q-d 2gvk-d 6p8s-2 3e5m-1 3tm8-2 4ztm-1 3vvh-1 5t1s-1 3e8n-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) 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	#152 - Aug 2012 cAMP-dependent Protein Kinase similarity (2)

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

hetero molecules

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

1

A: Uncharacterized protein

hetero molecules

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

2

B: Uncharacterized protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	47.100, 49.401, 78.372
Angle α, β, γ (deg.)	73.17, 75.90, 67.34
Int Tables number	1
Space group name H-M	P1

#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: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.15 Å³/Da / Density % sol: 42.83 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1M Bis Tris pH 5.5, 0.4M 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: 1.55→13.7 Å / Num. all: 89498 / Num. obs: 80548 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / R_merge(I) obs: 0.08 / Net I/σ(I): 13.4
Reflection shell	Resolution: 1.55→1.63 Å / % possible all: 62.9

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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: 1.55→13.669 Å / SU ML: 0.21 / σ(F): 2.01 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2355	4043	5.02 %	random
R_work	0.2095	-	-	-
all	0.2108	89498	-	-
obs	0.2108	80544	89.96 %	-

Solvent computation

Shrinkage radii: 0.04 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 60.358 Å² / k_sol: 0.531 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.2659 Å²	0.2061 Å²	0.1216 Å²
2-	-	3.0403 Å²	0.8999 Å²
3-	-	-	-0.7744 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→13.669 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4856	0	22	352	5230

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4991
X-RAY DIFFRACTION	f_angle_d	1.029	6747
X-RAY DIFFRACTION	f_dihedral_angle_d	12.606	1913
X-RAY DIFFRACTION	f_chiral_restr	0.074	758
X-RAY DIFFRACTION	f_plane_restr	0.004	880

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 (%)
1.55-1.5678	0.2628	79	0.2128	1367	X-RAY DIFFRACTION	46
1.5678-1.5869	0.253	92	0.2131	1868	X-RAY DIFFRACTION	64
1.5869-1.607	0.2865	96	0.2022	1951	X-RAY DIFFRACTION	67
1.607-1.6281	0.2156	110	0.2025	2084	X-RAY DIFFRACTION	70
1.6281-1.6504	0.2507	115	0.2058	2101	X-RAY DIFFRACTION	73
1.6504-1.6739	0.2141	103	0.1965	2267	X-RAY DIFFRACTION	76
1.6739-1.6988	0.2404	121	0.2039	2301	X-RAY DIFFRACTION	79
1.6988-1.7253	0.2488	127	0.1943	2426	X-RAY DIFFRACTION	82
1.7253-1.7536	0.265	137	0.2063	2510	X-RAY DIFFRACTION	86
1.7536-1.7837	0.2675	116	0.1981	2646	X-RAY DIFFRACTION	89
1.7837-1.8161	0.2694	160	0.2053	2680	X-RAY DIFFRACTION	92
1.8161-1.8509	0.249	148	0.2115	2766	X-RAY DIFFRACTION	95
1.8509-1.8886	0.2289	131	0.2027	2889	X-RAY DIFFRACTION	97
1.8886-1.9296	0.2302	172	0.211	2848	X-RAY DIFFRACTION	99
1.9296-1.9743	0.2615	167	0.2165	2933	X-RAY DIFFRACTION	99
1.9743-2.0236	0.2725	164	0.2209	2852	X-RAY DIFFRACTION	99
2.0236-2.0781	0.2466	128	0.2029	2900	X-RAY DIFFRACTION	99
2.0781-2.139	0.2303	151	0.2056	2972	X-RAY DIFFRACTION	99
2.139-2.2078	0.2387	150	0.1982	2860	X-RAY DIFFRACTION	99
2.2078-2.2864	0.2344	155	0.2044	2921	X-RAY DIFFRACTION	100
2.2864-2.3774	0.229	160	0.2078	2953	X-RAY DIFFRACTION	100
2.3774-2.485	0.2416	143	0.206	2941	X-RAY DIFFRACTION	100
2.485-2.6152	0.2558	142	0.2123	2951	X-RAY DIFFRACTION	100
2.6152-2.7778	0.2245	172	0.2214	2898	X-RAY DIFFRACTION	100
2.7778-2.9902	0.2264	155	0.2228	2923	X-RAY DIFFRACTION	100
2.9902-3.2873	0.2383	156	0.2268	2930	X-RAY DIFFRACTION	100
3.2873-3.7543	0.2109	155	0.2054	2924	X-RAY DIFFRACTION	100
3.7543-4.6979	0.2132	170	0.192	2921	X-RAY DIFFRACTION	100
4.6979-13.6693	0.2204	168	0.2275	2918	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	0.0103	-0.018	0.0177	0.0687	-0.0641	0.0606	-0.0065	0.003	-0.007	0.0602	-0.0041	0.0067	-0.0268	0.0277	0.0056	0.0415	-0.0017	0.0131	0.0333	0.0025	0.0193	11.6532	42.9684	37.8675
2	0.0694	0.0534	-0.0125	0.054	0.0061	0.0225	0.0241	0.0075	0.0593	0.0228	-0.0199	0.0295	-0.0119	0.0027	-0.0014	0.0129	0.0038	-0.0003	0.0263	-0.0022	0.0371	8.0256	46.4082	28.6839
3	0.1897	-0.095	-0.2383	0.0907	0.1238	0.3808	-0.0419	0.0184	-0.0101	0.0307	-0.0168	0.0085	0.047	-0.0318	0.0398	0.0076	0.0003	-0.006	0.0068	-0.0015	-0.0073	13.1712	38.6603	17.1654
4	0.3689	0.0466	-0.0087	0.017	0.0405	0.1642	0.0045	0.0071	0.0926	-0.0081	-0.0025	0.0035	-0.0246	0.0229	-0.0022	0.0208	0.0014	0.0017	0.0062	0.0014	0.0194	20.6856	51.9771	19.2901
5	0.0527	0.0058	-0.0449	0.0415	-0.0172	0.0424	-0.0031	0.0271	0.0037	-0.0089	-0.0044	0.0239	0.0067	-0.0259	-0.0069	-0.01	-0.0129	-0.0049	0.0146	0.008	0.0177	22.4983	44.1057	11.039
6	0.0293	-0.0044	-0.0004	0.011	-0.014	0.0266	0.0217	0.0118	-0.0761	0.014	-0.0243	0.0121	0.0115	0.0077	-0.0004	0.0621	0.0078	-0.0255	0.0189	-0.0203	0.0583	34.6607	33.6451	17.6725
7	0.0107	-0.0249	0.0118	0.1459	-0.0602	0.0519	-0.0029	0.0134	0.0122	0.0054	-0.0372	-0.0613	-0.0137	0.0298	0.015	-0.029	-0.0388	0.0209	-0.0379	0.0263	-0.0133	33.464	46.9153	10.5042
8	0.1352	-0.0154	0.0309	0.1068	0.058	0.134	-0.0061	0.0513	0.0213	0.0219	0.019	-0.0256	0.0516	0.017	-0.0146	0.0208	0.0026	-0.0005	0.0193	0.003	0.027	31.3906	16.0575	-1.4753
9	0.019	0.014	0.0049	0.0712	0.0076	0.1258	-0.0054	-0.008	-0.0028	0.0012	-0.0172	-0.0095	-0.0432	0.0285	0.0161	0.022	0.0015	0.0078	0.0087	0.006	0.0177	28.0979	25.7239	-14.5823
10	0.1266	0.0319	0.0296	0.0096	0.0097	0.0087	0.0043	0.0279	-0.0357	0.0031	0.0026	-0.0021	0.0062	0.0034	-0.0127	-0.0303	0.0084	-0.0194	-0.0147	-0.0202	-0.0209	17.5754	19.8665	-16.5964
11	0.04	-0.05	0.0063	0.1533	0.0627	0.0559	0.0134	0.0291	0.0107	-0.0007	-0.0053	-0.0445	-0.0049	-0.0234	-0.0116	-0.0102	-0.0034	-0	0.022	-0.0034	-0.0024	18.5832	31.5678	-18.1023
12	0.0606	-0.0323	-0.0309	0.018	0.0113	0.0486	0.0126	-0.0407	0.0686	-0.0028	0.008	-0.023	-0.0201	-0.0039	-0.0204	0.0613	-0.0094	0.0236	0.0423	-0.0303	0.0708	7.8271	35.267	-7.3141
13	0.0128	0.0162	0.0466	0.0531	0.1099	0.2486	-0.0073	-0.0022	0.0095	-0.0243	-0.027	0.0045	-0.0445	-0.0859	-0.0062	-0.0242	0.0299	-0.0163	0.0054	0.0104	-0.03	8.6368	32.2788	-19.2818
14	0.0167	0.0012	0.0001	0.0055	-0.0048	0.0121	0.013	0.0001	-0.0209	0.0062	0.0086	-0.0032	0.02	-0.0314	-0.0175	-0.0058	-0.013	-0.0242	0.0853	-0.0169	0.0037	3.8444	23.1221	-25.789

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 2:48)
2	X-RAY DIFFRACTION	2	(chain A and resid 49:91)
3	X-RAY DIFFRACTION	3	(chain A and resid 92:121)
4	X-RAY DIFFRACTION	4	(chain A and resid 122:160)
5	X-RAY DIFFRACTION	5	(chain A and resid 161:192)
6	X-RAY DIFFRACTION	6	(chain A and resid 193:223)
7	X-RAY DIFFRACTION	7	(chain A and resid 224:307)
8	X-RAY DIFFRACTION	8	(chain B and resid 2:82)
9	X-RAY DIFFRACTION	9	(chain B and resid 83:130)
10	X-RAY DIFFRACTION	10	(chain B and resid 131:162)
11	X-RAY DIFFRACTION	11	(chain B and resid 163:192)
12	X-RAY DIFFRACTION	12	(chain B and resid 193:225)
13	X-RAY DIFFRACTION	13	(chain B and resid 226:281)
14	X-RAY DIFFRACTION	14	(chain B and resid 282:307)

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