PDB-2p3p: Structure of a domain of an uncharacterized protein PG_1388 from ...

ID or keywords:

Entry

Database: PDB / ID: 2p3p

Title

Structure of a domain of an uncharacterized protein PG_1388 from Porphyromonas gingivalis W83

Components

Hypothetical protein

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / MCSG / hypothetical protein / MAD / PSI-2 / structure genomics / singleton / PG_1388 / Protein Structure Initiative / Midwest Center for Structural Genomics

Function / homology

Protein of unknown function DUF3256 / Protein of unknown function (DUF3256) / membrane => GO:0016020 / Uncharacterized protein

Function and homology information

Biological species

Porphyromonas gingivalis W83 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.76 Å

Authors

Nocek, B. / Hatzos, C. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Structure of a domain of an uncharacterized protein PG_1388 from Porphyromonas gingivalis W83
Authors: Nocek, B. / Hatzos, C. / Moy, S. / Joachimiak, A.

History

Deposition	Mar 9, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 10, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance

Remark 300

BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2p3p.cif.gz	107.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2p3p.ent.gz	89.6 KB	Display	PDB format
PDBx/mmJSON format	2p3p.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2p3p_validation.pdf.gz	434.9 KB	Display	wwPDB validaton report
Full document	2p3p_full_validation.pdf.gz	436.9 KB	Display
Data in XML	2p3p_validation.xml.gz	22 KB	Display
Data in CIF	2p3p_validation.cif.gz	34.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p3/2p3p ftp://data.pdbj.org/pub/pdb/validation_reports/p3/2p3p	HTTPS FTP

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Related structure data

Similar structure data	2b4m-2 3ds7-1 6m2c-4 6z3x-d 2fx0-d 2jjt-1 5y9p-d 3rkf-3 2ozz-2 6fsf-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
Other databases	TargetDB: APC90158.1

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Hypothetical protein

B: Hypothetical protein

hetero molecules

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

1

A: Hypothetical protein

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

2

B: Hypothetical protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	43.753, 48.259, 54.191
Angle α, β, γ (deg.)	86.55, 79.58, 68.35
Int Tables number	1
Space group name H-M	P1

#1: Protein	Hypothetical protein Mass: 23802.289 Da / Num. of mol.: 2 / Fragment: Targeted domain: residues 61-264 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyromonas gingivalis W83 (bacteria) Species: Porphyromonas gingivalis / Strain: W83, PG_1388 / Gene: PG_1388 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7MUU3
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 556 / 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: 2.2 Å³/Da / Density % sol: 43.99 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M Ammonium acetate, 0.1M BIS-TRIS pH 6.5, 25 % w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97924, 0.97938

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 5, 2007 / Details: mirrors

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97924	1
2	0.97938	1

Reflection

Resolution: 1.76→35 Å / Num. all: 37374 / Num. obs: 37374 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / B_iso Wilson estimate: 27.2 Å² / R_merge(I) obs: 0.07 / Net I/σ(I): 14.4

Reflection shell

Resolution: 1.76→1.79 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.19 / Mean I/σ(I) obs: 6 / % possible all: 71.7

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
MLPHARE		phasing
DM		phasing
SOLVE		phasing
RESOLVE		phasing
ARP/wARP		model building
CCP4		phasing
O		model building
Coot		model building

Refinement

Method to determine structure:

MAD / Resolution: 1.76→35 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.93 / SU B: 5.552 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.133 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22645	1873	5 %	RANDOM
R_work	0.16547	-	-	-
obs	0.16849	35455	92.89 %	-
all	-	35455	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 9.885 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.56 Å²	-0.27 Å²	-0.38 Å²
2-	-	0.33 Å²	0.41 Å²
3-	-	-	-0.6 Å²

Refinement step

Cycle: LAST / Resolution: 1.76→35 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3183	0	1	556	3740

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	3397
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2333
X-RAY DIFFRACTION	r_angle_refined_deg	1.566	1.954	4644
X-RAY DIFFRACTION	r_angle_other_deg	0.936	3	5651
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.187	5	424
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.31	22.5	160
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.458	15	572
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.251	15	35
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	528
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	3817
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	752
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	629
X-RAY DIFFRACTION	r_nbd_other	0.208	0.2	2509
X-RAY DIFFRACTION	r_nbtor_refined	0.182	0.2	1664
X-RAY DIFFRACTION	r_nbtor_other	0.084	0.2	1842
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.167	0.2	382
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.226	0.2	22
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.282	0.2	80
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.167	0.2	63
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.93	1.5	2493
X-RAY DIFFRACTION	r_mcbond_other	0.26	1.5	808
X-RAY DIFFRACTION	r_mcangle_it	1.195	2	3409
X-RAY DIFFRACTION	r_scbond_it	2.049	3	1471
X-RAY DIFFRACTION	r_scangle_it	2.784	4.5	1232
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.76→1.806 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.284	131	-
R_work	0.199	2416	-
obs	-	-	84.96 %

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	6.7036	4.1154	-1.4974	4.976	-0.798	2.2537	-0.1409	0.1315	-0.1105	-0.2579	0.0701	-0.15	0.0077	-0.0258	0.0708	0.0712	0.021	0.0135	0.0569	-0.0022	0.0401	47.4316	8.1624	26.952
2	3.1524	0.1178	-0.7344	14.5597	-0.9622	0.2311	0.0408	0.2808	0.0808	-0.193	-0.0714	0.2668	-0.4207	-0.1991	0.0306	0.0722	-0.0207	-0.0466	0.1132	0.0013	0.0325	37.5239	11.0619	27.9131
3	34.8737	20.0282	-18.1724	13.7367	-11.2725	23.4546	0.0165	0.7013	0.5745	-0.7576	0.2901	0.2855	-0.0388	-0.8458	-0.3066	0.1843	0.0488	-0.0402	0.0331	0.0192	0.0245	43.1772	19.8543	24.2354
4	6.5651	1.2958	-1.623	1.9643	-1.0397	2.5966	0.0051	0.1188	0.1116	-0.1035	0.0766	0.1272	0.033	-0.1806	-0.0818	0.0694	0.0085	-0.0164	0.0193	-0.001	0.0505	46.2671	21.8564	32.9472
5	20.3714	12.9161	10.3249	12.5742	7.9832	7.285	0.2417	-0.8589	0.4658	0.1676	-0.6836	0.3876	0.002	-0.9878	0.4419	0.0512	-0.0039	0.0026	0.1441	-0.0214	0.1378	31.3905	12.9989	36.2675
6	0.8711	-1.2511	0.2166	2.0199	-0.2115	1.6446	0.0029	0.1226	0.0654	-0.0402	0.0383	-0.0093	0.0166	-0.1036	-0.0411	0.0616	-0.0007	-0.005	0.0274	-0.0084	0.0637	48.4672	12.7966	37.0175
7	4.5006	-2.0897	-4.0204	2.2083	2.3638	6.3984	0.1379	0.0086	0.0731	-0.0349	0.0081	-0.0974	0.0069	-0.02	-0.146	0.0468	0.0028	0.0029	0.0255	-0.0012	0.0722	51.3511	3.9706	41.2236
8	6.3942	-3.3997	4.599	4.7844	-3.604	7.9391	0.0133	-0.1191	-0.1386	0.1757	0.3102	0.3144	0.2214	-0.0458	-0.3235	0.1073	0.0258	0.0038	0.0531	-0.0124	0.019	52.2762	-2.5661	31.7339
9	1.0863	-0.555	0.5287	0.5969	-0.2481	18.5569	0.0703	0.0195	-0.1322	-0.0184	-0.0761	-0.1151	0.8647	0.4367	0.0058	0.0985	0.0314	0.0167	0.0654	0.0285	0.0744	58.5048	-3.6108	48.2266
10	0.6113	-0.8517	0.7102	1.3014	-1.5536	3.5999	-0.0022	-0.0216	0.0266	-0.0233	-0.014	0.0012	0.1652	-0.0208	0.0162	0.0877	-0.0202	-0.0158	0.0851	-0.0002	0.0656	55.5031	-2.3752	65.8844
11	3.7395	1.1313	-3.0358	2.657	-2.7361	7.6802	0	0.0542	0.1334	0.0333	-0.0811	-0.1578	-0.2507	0.1877	0.0811	0.0414	-0.0064	-0.0073	0.0386	0.0046	0.0764	56.0999	9.6126	47.6832
12	6.001	2.5245	-0.8325	3.1385	8.593	38.6336	0.1368	0.0261	0.126	-0.1465	-0.0978	0.3711	-0.3218	-2.4793	-0.0389	0.055	0.0839	0.0133	0.22	0.0076	0.071	46.01	5.7176	67.5816
13	1.9826	-1.6644	-0.9189	2.3215	4.4074	14.7301	-0.0955	0.0827	0.119	0.0902	-0.1296	-0.1386	-0.4647	-0.1562	0.2251	0.078	-0.0045	-0.0233	0.0579	-0.0007	0.0547	55.5238	5.7235	67.311
14	1.8625	1.1227	-2.0044	2.7115	1.5753	14.3673	0.1375	-0.1632	-0.0863	-0.1118	0.0525	-0.3528	0.0239	0.6909	-0.19	0.0164	0.0371	0.011	0.0802	0.0116	0.1	64.0711	4.9942	44.6046
15	11.6481	-1.5105	14.1742	3.8133	-6.8735	34.6938	-0.0599	-0.0589	0.6212	0.0211	-0.3301	-0.7153	0.3282	0.9188	0.39	-0.0104	0.0557	0.05	0.0402	0.0508	0.1123	65.0706	2.2652	45.3668
16	4.8997	-2.2647	0.5752	6.2413	1.5918	3.6951	0.1124	-0.0626	0.0274	0.2587	-0.0668	-0.2238	-0.0847	0.0904	-0.0455	0.0882	-0.0452	-0.012	0.0302	-0.0163	0.0372	77.1093	-15.3743	56.1946
17	6.0292	-1.9049	4.4725	10.8696	-3.812	4.2889	0.1267	-0.6561	0.0192	0.304	0.0889	0.3798	-0.1135	-0.3915	-0.2155	0.0386	-0.0178	0.0714	0.0821	-0.0146	0.0432	67.3764	-19.5076	57.9085
18	6.5389	-1.6348	-2.8583	5.971	2.9212	6.9698	-0.0931	-0.2219	0.3129	0.3647	0.0927	-0.0073	0.2368	0.0093	0.0004	0.0634	-0.0018	-0.0377	0.0196	-0.0004	0.0551	79.6077	-26.8952	55.8227
19	4.3717	0.7017	-0.4792	6.0474	-0.9002	1.802	-0.0483	-0.1178	0.0867	0.1119	0.0782	0.4036	0.0416	-0.098	-0.0299	0.0565	-0.0073	0.0018	0.0418	-0.0102	0.0495	71.1472	-24.5082	49.5673
20	22.5542	-1.0734	2.5046	25.4644	-7.5136	16.4424	-0.2748	0.3006	-0.3388	-0.8781	0.7505	0.9471	0.787	-0.543	-0.4756	0.0872	-0.0397	-0.0171	0.0693	0.016	0.0978	63.9626	-21.5521	42.7293
21	12.7765	9.0066	2.9271	8.5765	1.8463	0.6918	-0.1011	0.2648	0.0929	-0.0271	0.1487	0.0674	-0.0113	0.1861	-0.0476	0.1404	-0.0334	0.0139	0.169	-0.013	0.0836	83.323	-10.0005	46.6788
22	8.4972	1.5197	7.2699	1.8132	1.7887	7.7259	0.0752	-0.1854	-0.0407	-0.0466	-0.0494	0.1994	-0.0548	-0.2987	-0.0258	0.0713	-0.0071	-0.0059	0.0423	0.0043	0.0711	67.8289	-12.9746	39.5402
23	0.9129	0.537	-0.3728	1.2976	-2.0893	6.2058	0.0101	-0.0676	0.1453	0.2136	-0.1237	0.1861	-0.3343	0.0098	0.1135	0.0825	-0.0095	-0.0008	0.0341	-0.0166	0.0768	76.1921	-3.3777	44.4639
24	6.5318	-1.1597	5.371	1.6912	-2.0487	5.4353	-0.1561	0.5294	0.2431	0.0584	-0.1702	-0.1674	-0.1842	0.4959	0.3263	0.0355	-0.0039	-0.0084	0.1201	-0.003	0.0348	69.0133	-3.4203	16.686
25	7.8414	-0.2541	1.7155	2.4429	3.0526	6.1752	0.0349	0.0218	0.0215	-0.0629	0.1208	-0.0192	-0.2106	0.1779	-0.1557	0.0649	0.0133	0.02	0.0416	-0.0445	0.0571	60.2979	-3.5743	19.4354
26	5.5752	-2.1633	2.7694	2.6691	-1.7729	3.9685	-0.0695	-0.0015	-0.0524	0.0411	-0.014	-0.1276	-0.0069	0.1507	0.0835	0.0505	-0.0011	-0.0015	0.0358	0.0072	0.057	74.7072	-14.0815	33.5704
27	18.1831	11.4208	7.1266	9.8134	10.6926	18.7972	-0.0852	-0.3638	-0.5223	-0.2842	0.1766	0.1465	1.0885	-0.1216	-0.0915	0.134	-0.0208	-0.0509	0.0279	0.0501	0.107	59.6406	-14.9297	22.3539
28	7.4315	-1.8531	7.5848	2.1966	-0.1085	9.5737	0.6618	0.2672	-0.8867	-0.0982	-0.1219	0.1187	0.5238	0.2149	-0.5399	0.0649	0.0195	-0.0197	0.0566	-0.0331	0.0875	65.9514	-12.4402	17.7239
29	1.4092	1.2639	2.9358	1.7469	2.5043	7.473	-0.019	0.2531	0.0396	0.0208	0.2622	-0.1794	-0.0216	0.617	-0.2431	0.0649	-0.0261	0.0027	0.1082	-0.006	0.0781	84.839	-6.5742	35.6455
30	12.3625	12.0825	0.6163	19.3445	9.3319	37.959	-0.4075	0.6738	-1.2963	-0.4186	0.8625	-1.4746	0.7962	1.1198	-0.455	0.0347	-0.002	0.0383	0.0824	-0.0566	0.1711	84.7938	-7.6998	26.9266

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	66 - 81	9 - 24
2	X-RAY DIFFRACTION	2	A	A	82 - 92	25 - 35
3	X-RAY DIFFRACTION	3	A	A	93 - 98	36 - 41
4	X-RAY DIFFRACTION	4	A	A	99 - 108	42 - 51
5	X-RAY DIFFRACTION	5	A	A	109 - 116	52 - 59
6	X-RAY DIFFRACTION	6	A	A	117 - 141	60 - 84
7	X-RAY DIFFRACTION	7	A	A	142 - 166	85 - 109
8	X-RAY DIFFRACTION	8	A	A	167 - 176	110 - 119
9	X-RAY DIFFRACTION	9	A	A	177 - 186	120 - 129
10	X-RAY DIFFRACTION	10	A	A	187 - 212	130 - 155
11	X-RAY DIFFRACTION	11	A	A	213 - 229	156 - 172
12	X-RAY DIFFRACTION	12	A	A	230 - 237	173 - 180
13	X-RAY DIFFRACTION	13	A	A	238 - 248	181 - 191
14	X-RAY DIFFRACTION	14	A	A	249 - 257	192 - 200
15	X-RAY DIFFRACTION	15	A	A	258 - 262	201 - 205
16	X-RAY DIFFRACTION	16	B	B	65 - 80	8 - 23
17	X-RAY DIFFRACTION	17	B	B	81 - 92	24 - 35
18	X-RAY DIFFRACTION	18	B	B	93 - 102	36 - 45
19	X-RAY DIFFRACTION	19	B	B	103 - 127	46 - 70
20	X-RAY DIFFRACTION	20	B	B	128 - 134	71 - 77
21	X-RAY DIFFRACTION	21	B	B	135 - 146	78 - 89
22	X-RAY DIFFRACTION	22	B	B	147 - 163	90 - 106
23	X-RAY DIFFRACTION	23	B	B	164 - 183	107 - 126
24	X-RAY DIFFRACTION	24	B	B	184 - 198	127 - 141
25	X-RAY DIFFRACTION	25	B	B	199 - 209	142 - 152
26	X-RAY DIFFRACTION	26	B	B	210 - 228	153 - 171
27	X-RAY DIFFRACTION	27	B	B	229 - 235	172 - 178
28	X-RAY DIFFRACTION	28	B	B	236 - 250	179 - 193
29	X-RAY DIFFRACTION	29	B	B	251 - 259	194 - 202
30	X-RAY DIFFRACTION	30	B	B	260 - 264	203 - 207

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