PDB-5mdo: Crystal structure of in vitro folded Chitoporin VhChip from Vibri...

ID or keywords:

Entry

Database: PDB / ID: 5mdo

Title

Crystal structure of in vitro folded Chitoporin VhChip from Vibrio harveyi (crystal form I)

Components

Chitoporin

Keywords

SUGAR BINDING PROTEIN /

outer membrane protein /

Vibrio harveyi /

Chitin /

porin

Function / homology

Gram-negative porin / Porin domain, Gram-negative type /

Porin, Gram-negative type / Porin domain superfamily /

porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane / Chitoporin

Function and homology information

Biological species

Vibrio harveyi (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.95 Å

Authors

Zahn, M. / van den Berg, B.

Citation

Journal: Nat Commun / Year: 2018
Title: Structural basis for chitin acquisition by marine Vibrio species.
Authors: Aunkham, A. / Zahn, M. / Kesireddy, A. / Pothula, K.R. / Schulte, A. / Basle, A. / Kleinekathofer, U. / Suginta, W. / van den Berg, B.

History

Deposition	Nov 13, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 20, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2018	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5mdo.cif.gz	837.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5mdo.ent.gz	721.6 KB	Display	PDB format
PDBx/mmJSON format	5mdo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/md/5mdo ftp://data.pdbj.org/pub/pdb/validation_reports/md/5mdo	HTTPS FTP

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Related structure data

Related structure data	5mdpC 5mdqC 5mdrC 5mdsC C: citing same article (ref.)
Similar structure data	1hxu-1 1bt9-1 5mdr-2 4lse-d 6rd3-2 4gcp-2 3k19-4 1opf-2 6zhp-1 3pou-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Chitoporin

B: Chitoporin

C: Chitoporin

D: Chitoporin

E: Chitoporin

F: Chitoporin

hetero molecules

241 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Chitoporin

B: Chitoporin

C: Chitoporin

hetero molecules

defined by author&software
121 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Chitoporin

E: Chitoporin

F: Chitoporin

hetero molecules

defined by author&software
120 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	146.884, 123.379, 147.026
Angle α, β, γ (deg.)	90.00, 117.89, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	A	10 - 350
2	1	B	10 - 350
1	2	A	10 - 350
2	2	C	10 - 350
1	3	A	10 - 350
2	3	D	10 - 350
1	4	A	10 - 350
2	4	E	10 - 350
1	5	A	10 - 350
2	5	F	10 - 350
1	6	B	10 - 350
2	6	C	10 - 350
1	7	B	10 - 350
2	7	D	10 - 350
1	8	B	10 - 350
2	8	E	10 - 350
1	9	B	10 - 350
2	9	F	10 - 350
1	10	C	10 - 350
2	10	D	10 - 350
1	11	C	10 - 350
2	11	E	10 - 350
1	12	C	10 - 350
2	12	F	10 - 350
1	13	D	10 - 350
2	13	E	10 - 350
1	14	D	10 - 350
2	14	F	10 - 350
1	15	E	10 - 350
2	15	F	10 - 350

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

#1: Protein	Chitoporin Mass: 39192.863 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio harveyi (bacteria) / Gene: chiP / Production host: Escherichia coli (E. coli) / References: UniProt: L0RVU0
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE Mass: 306.438 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C₁₆H₃₄O₅ / Comment: C8E, detergent*YM
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1796 / 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 grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 30% (w/v) PEG 400, 0.05 M NaCl, 0.1 M sodium citrate pH 5.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 25, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 1.95→64.97 Å / Num. obs: 336423 / % possible obs: 100 % / Redundancy: 6.8 % / R_merge(I) obs: 0.072 / R_pim(I) all: 0.046 / Net I/σ(I): 13.9
Reflection shell	Resolution: 1.95→1.98 Å / Redundancy: 6.7 % / R_merge(I) obs: 0.854 / R_pim(I) all: 0.543 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0131	refinement
XDS		data reduction
Aimless		data scaling
AutoSol		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.95→129.94 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.952 / SU B: 4.129 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.085 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1867	3124	0.9 %	RANDOM
R_work	0.16708	-	-	-
obs	0.16726	333266	99.95 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 37.76 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.09 Å²	-0 Å²	0.27 Å²
2-	-	1.48 Å²	0 Å²
3-	-	-	-1.08 Å²

Refinement step

Cycle: 1 / Resolution: 1.95→129.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15990	0	259	1796	18045

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.021	0.02	16684
X-RAY DIFFRACTION	r_bond_other_d	0.01	0.02	14623
X-RAY DIFFRACTION	r_angle_refined_deg	1.859	1.944	22515
X-RAY DIFFRACTION	r_angle_other_deg	1.429	3	33579
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	9.294	5.063	2057
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.359	24.812	906
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.945	15	2243
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.062	15	78
X-RAY DIFFRACTION	r_chiral_restr	0.128	0.2	2152
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.02	19774
X-RAY DIFFRACTION	r_gen_planes_other	0.008	0.02	4188
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	1.453	2.096	8198
X-RAY DIFFRACTION	r_mcbond_other	1.453	2.096	8197
X-RAY DIFFRACTION	r_mcangle_it	2.061	3.131	10244
X-RAY DIFFRACTION	r_mcangle_other	2.06	3.131	10245
X-RAY DIFFRACTION	r_scbond_it	2.641	2.516	8486
X-RAY DIFFRACTION	r_scbond_other	2.641	2.516	8487
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.981	3.613	12272
X-RAY DIFFRACTION	r_long_range_B_refined	8.466	20.419	20163
X-RAY DIFFRACTION	r_long_range_B_other	8.466	20.421	20164
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	37792	0.03
1	2	B	37792	0.03
2	1	A	37748	0.03
2	2	C	37748	0.03
3	1	A	37670	0.04
3	2	D	37670	0.04
4	1	A	37966	0.02
4	2	E	37966	0.02
5	1	A	38008	0.03
5	2	F	38008	0.03
6	1	B	37596	0.04
6	2	C	37596	0.04
7	1	B	37806	0.03
7	2	D	37806	0.03
8	1	B	37882	0.04
8	2	E	37882	0.04
9	1	B	37892	0.03
9	2	F	37892	0.03
10	1	C	37954	0.03
10	2	D	37954	0.03
11	1	C	37754	0.04
11	2	E	37754	0.04
12	1	C	37790	0.04
12	2	F	37790	0.04
13	1	D	37664	0.04
13	2	E	37664	0.04
14	1	D	37758	0.04
14	2	F	37758	0.04
15	1	E	38024	0.03
15	2	F	38024	0.03

LS refinement shell

Resolution: 1.95→2.001 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.231	212	-
R_work	0.245	24658	-
obs	-	-	99.96 %

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	0.5443	-0.1738	0.3847	6.5332	-2.8201	1.4064	0.0971	-0.0484	-0.2684	-0.1515	-0.013	-0.1029	0.1673	-0.0079	-0.0841	0.2909	0.0085	0.0127	0.2433	0.004	0.3027	-7.7221	-21.9811	57.6726
2	0.8082	-0.1604	0.0475	0.4909	-0.2923	1.0488	0.017	0.14	-0.0492	-0.1336	-0.0555	-0.0517	0.126	0.0954	0.0385	0.0609	0.0203	0.0105	0.2066	-0.0084	0.013	-2.7799	4.2642	34.1843
3	0.5097	-1.7865	-0.1488	6.4663	0.5143	0.0889	-0.0338	0.0048	-0.1562	0.0732	0.0014	0.3208	0.1359	0.0399	0.0324	0.385	0.0315	-0.0142	0.2556	0.0066	0.3192	-2.2473	-21.3952	64.2616
4	1.2029	-0.0944	0.1304	0.313	0.1048	1.0094	0.0081	-0.1361	0.0006	0.0713	0.0114	0.1278	0.0102	-0.1831	-0.0195	0.0314	-0.0186	0.0367	0.2199	0.0196	0.062	-24.8627	5.7752	68.2193
5	0.3223	1.3551	0.0438	6.7058	0.364	0.0434	-0.0317	0.0251	-0.1582	0.2075	-0.0042	-0.2226	0.0882	-0.0277	0.0359	0.3488	-0.0136	0.0396	0.2583	-0.0117	0.3589	0.7969	-21.8052	56.1801
6	1.0285	0.1971	0.2191	0.3044	0.0195	1.284	0.0099	-0.0741	0.0472	0.1046	-0.0491	-0.0908	-0.0189	0.1668	0.0392	0.0458	-0.0022	-0.0454	0.2297	0.0365	0.0583	15.5958	7.2854	70.2484
7	0.1548	-0.622	-0.2049	5.5581	1.1455	0.3244	0.1203	-0.0235	0.1451	-0.2873	-0.0369	0.072	-0.2035	0.0093	-0.0834	0.3365	-0.0189	0.0236	0.2496	-0.0057	0.3775	11.939	85.5916	24.6234
8	0.9785	0.0049	0.1412	0.293	0.1216	1.0988	-0.0109	0.2056	-0.0029	-0.1108	-0.0027	0.0015	0.0548	0.0502	0.0136	0.0728	0.0054	-0.0084	0.2278	0.0124	0.0054	6.1653	56.3914	5.184
9	0.687	-1.9596	0.764	5.8857	-1.8237	1.4355	-0.0517	0.001	0.1329	-0.0018	-0.0454	-0.2651	-0.3359	-0.0935	0.0971	0.2856	-0.0069	0.0206	0.2457	0.0039	0.308	6.6459	85.9148	31.4221
10	1.2463	-0.0845	0.1015	0.303	-0.2068	1.1481	0.0421	-0.011	0.0326	0.0393	-0.0683	-0.1376	-0.0121	0.1938	0.0262	0.0281	-0.0341	-0.0333	0.2052	0.0184	0.0804	29.4039	59.4526	38.2282
11	0.3252	1.4015	-0.248	7.3132	-1.5297	0.3681	-0.0346	0.0355	0.144	0.2374	0.015	0.1696	-0.1632	0.0244	0.0196	0.3408	-0.0088	-0.0288	0.2468	0.0139	0.334	3.4227	85.2594	23.4755
12	0.848	0.3176	0.0036	0.5339	-0.0074	0.9875	0.0519	-0.1305	0.0819	0.134	-0.0413	0.0954	-0.0836	-0.1177	-0.0106	0.0419	0.0061	0.0258	0.1996	-0.0236	0.0349	-11.018	58.4773	41.9047

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	10 - 20
2	X-RAY DIFFRACTION	2	A	21 - 350
3	X-RAY DIFFRACTION	3	B	10 - 20
4	X-RAY DIFFRACTION	4	B	21 - 350
5	X-RAY DIFFRACTION	5	C	10 - 20
6	X-RAY DIFFRACTION	6	C	21 - 350
7	X-RAY DIFFRACTION	7	D	10 - 20
8	X-RAY DIFFRACTION	8	D	21 - 350
9	X-RAY DIFFRACTION	9	E	10 - 20
10	X-RAY DIFFRACTION	10	E	21 - 350
11	X-RAY DIFFRACTION	11	F	10 - 20
12	X-RAY DIFFRACTION	12	F	21 - 350

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