PDB-3kdq: Crystal structure of a functionally unknown conserved protein fro...

ID or keywords:

Entry

Database: PDB / ID: 3kdq

Title

Crystal structure of a functionally unknown conserved protein from Corynebacterium diphtheriae.

Components

uncharacterized conserved protein

Keywords

structural genomics / unknown function / functionally unknown protein / Corynebacterium diphtheriae / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG

Function / homology

Ferritin / Ferritin - #10 / Helix non-globular / Special / Uncharacterized protein

Function and homology information

Biological species

Corynebacterium diphtheriae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 3 Å

Authors

Zhang, R. / Wu, R. / Tan, K. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of a functionally unknown conserved protein from Corynebacterium diphtheriae.
Authors: Zhang, R. / Wu, R. / Tan, K. / Clancy, S. / Joachimiak, A.

History

Deposition	Oct 23, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 10, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3kdq.cif.gz	259.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3kdq.ent.gz	219.7 KB	Display	PDB format
PDBx/mmJSON format	3kdq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3kdq_validation.pdf.gz	451.6 KB	Display	wwPDB validaton report
Full document	3kdq_full_validation.pdf.gz	472.7 KB	Display
Data in XML	3kdq_validation.xml.gz	23.8 KB	Display
Data in CIF	3kdq_validation.cif.gz	31.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kd/3kdq ftp://data.pdbj.org/pub/pdb/validation_reports/kd/3kdq	HTTPS FTP

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Related structure data

Similar structure data	1pyg-d 6w6g-d 3e3n-6 4621 3e3o-d 1noi-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: APC82872

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: uncharacterized conserved protein

B: uncharacterized conserved protein

C: uncharacterized conserved protein

D: uncharacterized conserved protein

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

1

A: uncharacterized conserved protein

B: uncharacterized conserved protein

C: uncharacterized conserved protein

D: uncharacterized conserved protein

A: uncharacterized conserved protein

B: uncharacterized conserved protein

C: uncharacterized conserved protein

D: uncharacterized conserved protein

A: uncharacterized conserved protein

B: uncharacterized conserved protein

C: uncharacterized conserved protein

D: uncharacterized conserved protein

A: uncharacterized conserved protein

B: uncharacterized conserved protein

C: uncharacterized conserved protein

D: uncharacterized conserved protein

defined by software
289 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	77.676, 132.484, 176.314
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
4	1

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	chain A and (resseq 0:28 or resseq 39:52 or resseq...
2	1	1	chain B and (resseq 0:28 or resseq 39:52 or resseq...
3	1	1	chain C and (resseq 0:28 or resseq 39:52 or resseq...
4	1	1	chain D and (resseq 0:28 or resseq 39:52 or resseq...

Details

Experimentally unknown. It is predicted that the four chains (A,B,C and D)and their symmetry-related molecules generated by operators (1-x,y,-z), (1-x,-y,z) and (1+x,-y,-z) respectively, form an assemble of sixteen molecules.

#1: Protein	uncharacterized conserved protein Mass: 18036.750 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Gene: Corynebacterium diphtheriae, DIP1984 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6NFB0

#1: Protein

uncharacterized conserved protein

Mass: 18036.750 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Corynebacterium diphtheriae (bacteria) / Gene: Corynebacterium diphtheriae, DIP1984 / Plasmid: pMCSG7 / Production host:

Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6NFB0

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.14 Å³/Da / Density % sol: 60.87 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Na-Hepes, 200mM Na Nitrate, 30% PEG400 , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97940, 0.97953

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2009 / Details: mirror

Radiation

Monochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9794	1
2	0.97953	1

Reflection

Resolution: 3→48.5 Å / Num. all: 18599 / Num. obs: 18599 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / R_merge(I) obs: 0.095 / Net I/σ(I): 29

Reflection shell

Resolution: 3→3.05 Å / Redundancy: 7 % / R_merge(I) obs: 0.679 / Mean I/σ(I) obs: 3.1 / Num. unique all: 895 / % possible all: 100

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
SHELXD		phasing
MLPHARE		phasing
DM		model building
RESOLVE		model building
HKL-3000		phasing
PHENIX	(phenix.refine: 1.5_2)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
DM		phasing
RESOLVE		phasing

Refinement

Method to determine structure:

MAD / Resolution: 3→48.461 Å / SU ML: 0.39 / σ(F): 1.88 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2643	1796	5.12 %	random
R_work	0.1971	-	-	-
all	0.2006	35075	-	-
obs	0.2006	35075	99.67 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 55.758 Å² / k_sol: 0.327 e/Å³

Refinement step

Cycle: LAST / Resolution: 3→48.461 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4939	0	0	0	4939

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	4979
X-RAY DIFFRACTION	f_angle_d	1.271	6719
X-RAY DIFFRACTION	f_dihedral_angle_d	21.198	1931
X-RAY DIFFRACTION	f_chiral_restr	0.081	781
X-RAY DIFFRACTION	f_plane_restr	0.003	887

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	907	X-RAY DIFFRACTION	POSITIONAL
1	2	B	907	X-RAY DIFFRACTION	POSITIONAL	0.04
1	3	C	896	X-RAY DIFFRACTION	POSITIONAL	0.04
1	4	D	907	X-RAY DIFFRACTION	POSITIONAL	0.043

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 (%)
2.9997-3.1069	0.3682	179	0.2996	3284	X-RAY DIFFRACTION	99
3.1069-3.2313	0.3729	195	0.2991	3318	X-RAY DIFFRACTION	100
3.2313-3.3783	0.4046	181	0.2751	3328	X-RAY DIFFRACTION	100
3.3783-3.5564	0.3371	175	0.2483	3361	X-RAY DIFFRACTION	100
3.5564-3.7791	0.2941	204	0.2189	3308	X-RAY DIFFRACTION	100
3.7791-4.0708	0.2517	160	0.1799	3329	X-RAY DIFFRACTION	100
4.0708-4.4802	0.2523	181	0.1676	3358	X-RAY DIFFRACTION	100
4.4802-5.1279	0.1927	196	0.1445	3313	X-RAY DIFFRACTION	100
5.1279-6.4582	0.2718	178	0.1896	3334	X-RAY DIFFRACTION	100
6.4582-48.4677	0.1901	147	0.1621	3346	X-RAY DIFFRACTION	99

Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

ID	Method	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	refined	1.3606	-0.9889	0.2707	1.4539	-1.0887	0.7678	0.0057	1.2827	0.5273	0.2787	-0.814	0.0174	-0.0866	0.4581	0.6295	0.3169	-0.1013	-0.0847	0.6983	-0.2841	0.7701	66.0524	31.091	38.2054
2		5.1426	-3.0586	2.1287	6.1634	-0.4309	1.0895	1.4461	0.7947	0.107	-0.6944	-1.2915	-0.1217	-0.1642	-0.5156	0.1565	0.3248	0.3923	0.0876	0.7165	-0.1099	0.4605
3		1.7492	0.6525	0.8613	2.6461	0.5613	0.262	-0.2786	-0.0713	0.5683	0.5363	0.1237	-0.5635	0.006	0.0767	0.0777	0.5016	-0.2517	-0.077	0.474	-0.1009	0.797
4		8.2383	-4.3055	6.1523	4.3699	-4.1637	5.0885	-0.7869	-0.8232	-0.9558	-0.7623	0.4711	-1.5223	0.1208	-0.5002	0.3035	0.5862	0.1817	-0.1056	0.5041	-0.1362	1.3751
5		1.2562	0.5217	-0.1207	0.2375	-0.2692	1.1976	-0.1309	0.0945	0.0115	-0.2732	0.4857	-0.221	-0.2159	-0.0051	-0.3354	0.621	0.0199	0.0136	0.2206	-0.1856	0.8845
6		2.1264	1.202	1.3038	5.0799	3.975	3.7074	-0.9094	0.1627	0.6113	0.4412	1.5138	0.3805	0.0967	0.5108	-0.1264	0.2905	-0.2699	-0.0256	0.1959	0.0873	0.6578
7		2.6452	-1.6528	0.2753	1.9851	-0.1422	0.6754	0.204	0.6226	0.2867	0.6339	0.1894	-0.429	0.2433	0.1291	-0.2878	0.5303	0.0649	-0.0693	0.2949	-0.0325	0.7105
8		1.4191	-0.8776	1.9643	0.8399	-0.809	2.8467	0.0464	-0.2249	-0.8686	0.0067	0.4619	0.5625	0.1254	-0.1323	-0.4671	0.2214	0.0855	0.0553	0.6308	-0.2984	0.6499
9		6.2878	-1.3897	5.7342	1.0407	0.0682	8.5465	2.4174	-1.0299	-2.2542	-0.4033	0.3691	-0.6624	-0.2254	-0.0785	-2.1277	0.0857	-0.0828	-0.5487	0.5401	0.144	0.6998
10		3.5284	-0.0341	-0.8751	0.0682	0.1457	0.4423	0.2473	-1.047	0.1862	0.0499	-0.0889	0.0263	-0.1611	-0.5711	-0.0242	0.4807	0.2188	0.1846	0.8625	-0.1403	0.4101
11		3.9906	0.9943	-5.0457	4.5008	-4.4355	8.7425	-1.2886	-1.9075	1.3824	-1.5491	0.2596	-1.0223	-0.3601	0.9715	0.5958	0.3016	-0.0976	-0.0911	1.5454	-0.4284	0.2533
12		3.2102	-0.5671	-1.5776	1.785	1.2337	1.0618	0.1242	0.723	-0.3168	-0.2014	-0.5501	0.2017	-0.2413	-0.7048	0.3166	0.3078	0.0742	-0.0306	0.7638	-0.1699	0.1838
13		1.6899	-0.9758	-1.7138	0.5674	0.9048	1.5975	-0.331	-0.7721	-0.0493	0.515	0.1	-0.1724	0.4901	0.942	0.171	0.2012	0.1336	0.2727	0.763	0.0433	0.2993
14		2.8094	-0.4342	2.3676	1.2116	-0.3729	2.0096	0.2075	-0.9158	-0.3501	0.038	-0.2985	0.1148	-0.3286	-0.1809	0.0988	0.4203	0.0726	-0.0813	0.7782	-0.0508	0.2949
15		4.9433	3.414	5.5444	4.005	4.9404	8.0067	0.3686	-0.5192	-1.44	0.2301	0.713	-0.9163	0.118	-0.6711	-0.8912	0.2742	0.117	0.0199	0.3396	0.0015	0.6618
16		3.0024	0.2027	-0.1454	8.0007	8.7319	9.3127	1.7819	-0.6744	-1.9891	0.2882	-2.2767	-0.8711	-0.1891	-1.9245	0.6374	0.2045	-0.4685	-0.0245	0.6244	-0.182	0.7151
17		5.9966	1.4225	1.8636	2.6779	2.3609	2.3724	-0.0791	-0.3218	1.7721	-0.4386	-0.2242	0.6239	-0.4002	-0.2025	0.1814	0.4606	0.2536	0.0979	0.4451	-0.2816	0.8179
18		4.7384	-1.6382	1.7389	0.8029	-0.9711	2.0049	0.7398	-0.246	1.0313	1.153	-1.7511	1.6912	1.2781	-0.0443	0.5597	0.8508	-0.0586	0.0109	0.4719	-0.5709	1.3184
19		1.2401	-0.7504	-0.1208	0.4512	0.0904	1.9532	0.0381	0.4699	-0.0849	0.2963	-0.4991	0.2442	0.5106	-0.24	0.4395	0.4241	-0.0528	-0.003	0.3254	-0.3311	0.8713
20		5.4782	-1.0826	-5.1283	1.3375	0.6408	5.3046	1.3443	-0.6058	1.485	-0.0223	1.184	0.6482	-1.1737	-0.2687	-0.4487	-0.246	-0.0669	-0.8219	0.4891	-0.3537	-0.0829
21		5.2063	-1.6539	-2.7386	3.3732	2.1074	2.2405	-0.2595	-0.4885	-0.0725	-0.0828	-0.1214	0.6315	0.1797	0.1731	0.246	0.4143	0.0599	-0.1099	0.3365	-0.2834	0.4636
22		0.4229	0.6401	0.2041	1.2317	0.3771	0.9507	0.0853	0.2946	0.6101	-0.5049	-0.4155	-0.3169	-0.5163	-0.2107	0.1548	0.0972	0.0078	-0.1517	0.7596	-0.0618	0.3423
23		5.5361	2.5875	-1.4178	4.8592	5.2036	9.2797	1.8875	0.7711	0.4784	0.7862	0.5607	-2.2411	0.0749	-1.9267	-1.6103	0.1308	0.1654	0.3263	0.4361	-0.0185	0.6484
24		8.7215	-4.838	-4.0739	3.7326	3.6895	4.0703	-0.3717	-1.7413	0.9934	0.4211	0.7245	-0.7722	0.2088	0.6626	-0.4572	0.5041	-0.0429	-0.2348	0.7969	-0.2583	0.4876
25		3.0206	2.0441	2.1284	6.8551	5.2387	7.3007	0.5493	0.5593	-0.2427	0.4267	-0.6273	0.8245	0.4522	1.3003	-0.4515	0.9681	-0.1175	0.1754	0.7453	-0.5532	0.6446
26		2.3053	0.9698	1.6187	0.8877	0.2438	6.2709	0.4996	0.2967	-0.3788	-0.0543	0.3412	-0.3271	0.6719	0.8416	-0.7811	0.3439	0.0413	-0.0018	0.7461	-0.2839	0.381
27		0.6813	-0.9744	0.4852	1.0127	0.1172	2.0651	0.1514	0.1858	0.5356	0.244	-0.5821	-0.2661	-0.1154	0.5608	-0.2367	-0.0118	0.0893	0.13	0.432	-0.2017	0.2872
28		2.9742	1.9251	3.8193	3.5344	3.7838	5.9843	0.2339	0.3604	0.2552	-0.2251	0.1669	-0.2214	0.0482	0.5046	-0.2439	0.3989	0.0986	0.0331	0.6796	-0.321	0.5088

Refinement TLS group

Selection details: chain D resid 120:151

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