PDB-5iqj: 1.9 Angstrom Crystal Structure of Protein with Unknown Function f...

ID or keywords:

Entry

Database: PDB / ID: 5iqj

Title

1.9 Angstrom Crystal Structure of Protein with Unknown Function from Vibrio cholerae.

Components

Uncharacterized protein

Keywords

UNKNOWN FUNCTION / CSGID / Vibrio cholerae / Structural Genomics / Center for Structural Genomics of Infectious Diseases

Function / homology

ACETATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / TARTRONATE / Uncharacterized protein

Function and homology information

Biological species

Vibrio cholerae O1 biovar El Tor (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.9 Å

Authors

Minasov, G. / Wawrzak, Z. / Stogios, P.J. / Skarina, T. / Seed, K.D. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: 1.9 Angstrom Crystal Structure of Protein with Unknown Function from Vibrio cholerae.
Authors: Minasov, G. / Wawrzak, Z. / Stogios, P.J. / Skarina, T. / Seed, K.D. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases

History

Deposition	Mar 10, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 23, 2016	Provider: repository / Type: Initial release
Revision 1.1	Mar 6, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_prerelease_seq / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5iqj.cif.gz	186.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5iqj.ent.gz	150.8 KB	Display	PDB format
PDBx/mmJSON format	5iqj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5iqj_validation.pdf.gz	521.8 KB	Display	wwPDB validaton report
Full document	5iqj_full_validation.pdf.gz	526.8 KB	Display
Data in XML	5iqj_validation.xml.gz	22.2 KB	Display
Data in CIF	5iqj_validation.cif.gz	32.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iq/5iqj ftp://data.pdbj.org/pub/pdb/validation_reports/iq/5iqj	HTTPS FTP

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Related structure data

Similar structure data	5e8a-d 1ii3-d 2f0u-d 4zy8-4 2ahd-4 4ygt-d 2f0m-d 6l6a-d 4id6-d 4als-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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-idp92786

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

C: Uncharacterized protein

hetero molecules

46.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Uncharacterized protein

hetero molecules

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

2

B: Uncharacterized protein

hetero molecules

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

3

C: Uncharacterized protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	45.126, 149.512, 159.966
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

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Protein , 1 types, 3 molecules ABC

#1: Protein	Uncharacterized protein Mass: 15042.494 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria) Plasmid: pMCSG53 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: M1QWM5

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Non-polymers , 9 types, 417 molecules

#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-TTN / TARTRONATE Mass: 118.045 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₂O₅
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#7: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#8: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#9: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#10: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 401 / 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: 3.01 Å³/Da / Density % sol: 59.1 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Protein: 7.0 mg/ml, 0.3M Sodium chloride, 0.01M HEPES (pH 7.5); Screen: 2M Ammonium sulfate, 0.1M HEPES (pH 7.5), 2% (w/v) PEG 400, 1% P300;

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 18, 2015 / Details: C(111)
Radiation	Monochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 1.9→29.41 Å / Num. obs: 42909 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / B_iso Wilson estimate: 28.8 Å² / CC_1/2: 0.873 / R_merge(I) obs: 0.067 / R_sym value: 0.067 / Net I/σ(I): 20.3
Reflection shell	Resolution: 1.9→1.93 Å / Redundancy: 5.1 % / R_merge(I) obs: 0.586 / Mean I/σ(I) obs: 2.9 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.9→29.41 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.934 / SU B: 6.129 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.135 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2292	2188	5.1 %	RANDOM
R_work	0.18074	-	-	-
obs	0.18315	40681	99.6 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 35.364 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.13 Å²	0 Å²	0 Å²
2-	-	-2.39 Å²	0 Å²
3-	-	-	1.26 Å²

Refinement step

Cycle: 1 / Resolution: 1.9→29.41 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3079	0	75	401	3555

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	3416
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3038
X-RAY DIFFRACTION	r_angle_refined_deg	1.315	1.951	4673
X-RAY DIFFRACTION	r_angle_other_deg	0.86	3	7029
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.032	5	424
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.545	26.739	184
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.408	15	537
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.303	15	3
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	520
X-RAY DIFFRACTION	r_gen_planes_refined	0.024	0.02	4018
X-RAY DIFFRACTION	r_gen_planes_other	0.02	0.02	759
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	1.471	2.048	1658
X-RAY DIFFRACTION	r_mcbond_other	1.471	2.046	1656
X-RAY DIFFRACTION	r_mcangle_it	2.274	3.046	2094
X-RAY DIFFRACTION	r_mcangle_other	2.274	3.046	2095
X-RAY DIFFRACTION	r_scbond_it	2.002	2.429	1757
X-RAY DIFFRACTION	r_scbond_other	1.99	2.421	1754
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.058	3.51	2577
X-RAY DIFFRACTION	r_long_range_B_refined	7.27	18.831	4375
X-RAY DIFFRACTION	r_long_range_B_other	7.025	17.762	4165
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.903→1.952 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.282	166	-
R_work	0.251	2822	-
obs	-	-	95.74 %

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	8.2313	-0.6397	-7.6421	3.0187	1.8509	10.756	0.0038	-0.7434	-0.1805	0.2086	-0.1974	0.2545	0.3615	0.2869	0.1936	0.2914	-0.0693	0.0049	0.2007	0.0342	0.0371	15.203	21.1286	80.5242
2	2.7948	0.3615	0.0351	4.5815	1.0098	1.0828	0.0556	-0.0669	-0.028	0.2652	-0.077	-0.0531	0.1733	-0.1237	0.0214	0.1546	-0.0768	0.0334	0.0501	-0.0215	0.0125	16.0776	27.6317	67.0802
3	11.2908	-4.7355	8.9535	1.9866	-3.7203	11.1282	-0.1106	0.017	-0.0312	0.043	-0.0055	0.0139	-0.1308	0.4266	0.1161	0.1407	-0.0164	-0.0583	0.0997	0.0719	0.0777	27.3585	16.7453	77.6919
4	2.5526	0.9953	1.0689	3.3091	1.3597	0.772	0.0188	-0.1284	0.0695	0.0936	-0.026	-0.236	0.0764	-0.0837	0.0072	0.2444	-0.0283	0.0524	0.2249	-0.0238	0.21	21.0872	34.4245	67.17
5	3.5335	-0.4736	0.4082	8.2719	4.2099	4.7151	-0.1444	-0.3895	-0.1865	0.4133	0.1195	-0.3384	0.3007	0.2781	0.0249	0.1042	0.0424	-0.0522	0.0793	0.0378	0.0867	29.6602	36.4913	75.3244
6	1.763	1.553	-0.0235	4.2972	0.2135	1.0538	-0.0464	0.1017	0.1396	0.2966	-0.0472	0.0932	0.2076	0.0118	0.0937	0.1012	-0.0238	0.0143	0.0668	0.0048	0.0218	18.6423	37.6401	69.5231
7	2.548	2.0253	-2.4574	8.6087	-4.9475	5.8636	-0.1431	0.2486	-0.0376	-0.2466	-0.0158	-0.0894	0.42	0.3417	0.1589	0.0872	0.0228	0.0368	0.1664	-0.0234	0.0837	18.7971	-6.3695	49.3747
8	2.3594	0.1405	-0.0574	4.3095	1.048	1.6805	0.0059	-0.0511	0.0266	0.0315	0.0687	-0.0316	0.0709	0.0788	-0.0746	0.0393	-0.024	0.0263	0.0452	-0.0098	0.0404	9.4911	2.985	58.0245
9	1.0349	-0.0045	0.4487	0.1315	1.0322	9.8777	0.0655	0.1522	-0.1361	-0.0509	0.0069	0.037	-0.12	0.1246	-0.0724	0.1466	-0.0242	-0.029	0.0931	-0.0421	0.1084	9.357	-5.3938	41.6539
10	2.41	1.1976	0.4922	4.5583	-1.0209	1.7368	0.026	0.0196	0.0999	-0.0418	-0.0436	0.0573	-0.0635	0.1321	0.0177	0.0259	-0.0162	0.0178	0.0491	-0.0182	0.0224	11.2537	10.725	54.7354
11	6.6759	1.8696	-0.8717	4.8487	-0.2817	4.6999	0.0513	0.5105	-0.1221	-0.4141	-0.0488	0.1749	-0.1242	-0.0652	-0.0025	0.119	-0.0087	-0.0054	0.108	-0.0201	0.0165	12.2521	14.2593	45.2077
12	0.3826	-0.6096	0.0788	4.1329	-1.1031	1.6792	0.0487	0.0683	-0.0961	0.0439	-0.0515	-0.3112	-0.1677	0.1617	0.0029	0.0878	-0.0331	0.0307	0.1624	-0.0345	0.1494	17.5605	10.1639	58.2274
13	8.3198	-4.5151	-5.1387	10.6382	11.3344	12.0942	-0.0365	0.6572	-0.0845	-0.2313	-0.5013	0.5282	-0.2335	-0.5689	0.5378	0.0524	-0.0321	-0.1337	0.2726	0.0829	0.3488	3.3985	53.1446	54.9327
14	3.7305	1.2391	-0.7403	4.9804	-0.4909	2.9763	-0.0603	0.0547	-0.0219	-0.0534	0.0772	0.5197	-0.0567	-0.2441	-0.0168	0.0321	-0.0138	-0.0417	0.058	0.0324	0.111	13.8608	53.5904	62.7066
15	4.0732	0.7275	0.3568	3.198	0.0123	3.4984	0.1221	-0.0865	0.1285	-0.063	-0.0308	0.1491	-0.0433	-0.241	-0.0913	0.0325	0.0015	-0.0102	0.0539	0.0353	0.0459	15.3306	66.279	60.6691
16	1.8164	-0.0487	-0.5263	3.0219	0.2991	1.4445	0.0346	-0.0481	0.1885	-0.1072	0.1088	0.3739	-0.0467	-0.1626	-0.1433	0.0609	-0.0198	-0.0528	0.1177	0.0543	0.1185	13.7163	66.5727	61.1603

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 5
2	X-RAY DIFFRACTION	2	A	6 - 32
3	X-RAY DIFFRACTION	3	A	33 - 45
4	X-RAY DIFFRACTION	4	A	46 - 76
5	X-RAY DIFFRACTION	5	A	77 - 96
6	X-RAY DIFFRACTION	6	A	97 - 131
7	X-RAY DIFFRACTION	7	B	1 - 6
8	X-RAY DIFFRACTION	8	B	7 - 31
9	X-RAY DIFFRACTION	9	B	32 - 46
10	X-RAY DIFFRACTION	10	B	47 - 76
11	X-RAY DIFFRACTION	11	B	77 - 103
12	X-RAY DIFFRACTION	12	B	104 - 131
13	X-RAY DIFFRACTION	13	C	2 - 6
14	X-RAY DIFFRACTION	14	C	7 - 52
15	X-RAY DIFFRACTION	15	C	53 - 78
16	X-RAY DIFFRACTION	16	C	79 - 131

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