PDB-4d5b: Crystal structure of CymA from Klebsiella oxytoca

ID or keywords:

Entry

Database: PDB / ID: 4d5b

Title

Crystal structure of CymA from Klebsiella oxytoca

Components

CYMA

Keywords

TRANSPORT PROTEIN / OUTER MEMBRANE CHANNEL / CYCLODEXTRIN TRANSPORT / BETA BARREL

Function / homology

Cyclodextrin porin CymA / Putative cyclodextrin porin / import into cell / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / alpha-cyclodextrin / CymA protein

Function and homology information

Biological species

KLEBSIELLA OXYTOCA (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.702 Å

Authors

van den Berg, B. / Bhamidimarri, S.P. / Kleinekathoefer, U. / Winterhalter, M.

Citation

Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2015
Title: Outer-membrane translocation of bulky small molecules by passive diffusion.
Authors: van den Berg, B. / Prathyusha Bhamidimarri, S. / Dahyabhai Prajapati, J. / Kleinekathofer, U. / Winterhalter, M.

History

Deposition	Nov 3, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 3, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jun 10, 2015	Group: Database references / Source and taxonomy
Revision 1.2	Jun 24, 2015	Group: Database references
Revision 1.3	Feb 21, 2018	Group: Advisory / Database references / Structure summary Category: audit_author / citation ...audit_author / citation / citation_author / pdbx_unobs_or_zero_occ_atoms Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 2.0	Jul 29, 2020	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _struct_asym.entity_id Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	Dec 20, 2023	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ...

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4d5b.cif.gz	304.7 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d5/4d5b ftp://data.pdbj.org/pub/pdb/validation_reports/d5/4d5b	HTTPS FTP

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Related structure data

Related structure data	4d51C 4d5dC 4v3gSC 4v3hC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4d5d-2 4d5d-1 4v3g-1 4v3g-2 4v3h-2 4v3h-1 4d51-d 3ljp-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
Related items in Molecule of the Month	#244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #59 - Nov 2004 Photosystem II similarity (1)

Deposited unit

A: CYMA

B: CYMA

hetero molecules

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

1

A: CYMA

hetero molecules

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

2

B: CYMA

hetero molecules

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

Unit cell

Length a, b, c (Å)	140.559, 77.397, 110.792
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-2116- HOH

#1: Protein

CYMA

Mass: 39905.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CLONING REGION INCLUDING HEPTAHISTIDINE TAG AT N-TERMINUS
Source: (gene. exp.)

KLEBSIELLA OXYTOCA (bacteria) / Plasmid: PB22 / Production host:

ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): C43 / Variant (production host): DELTA CYOABCD / References: UniProt: Q48391

#2: Polysaccharide

Cyclohexakis-(1-4)-(alpha-D-glucopyranose) / alpha-cyclodextrin

Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 990.860 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: alpha-cyclodextrin

#3: Chemical

...
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE

Mass: 306.438 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C₁₆H₃₄O₅ / Comment: C8E, detergent*YM

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 785 / 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: 3.8 Å³/Da / Density % sol: 68 % / Description: NONE
Crystal grow	pH: 7.5 Details: MORPHEUS 1/30. 0.09 M NPS, 0.1 M BUFFER SYSTEM 2 PH 7.5, 20% ETHYLENE GLYCOL, 10% PEG 8000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9796 Å / Relative weight: 1
Reflection	Resolution: 1.7→47 Å / Num. obs: 133006 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / B_iso Wilson estimate: 22.2 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 15
Reflection shell	Resolution: 1.7→1.73 Å / Redundancy: 7.4 % / R_merge(I) obs: 1.03 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4V3G

4v3g

Resolution: 1.702→45.047 Å / SU ML: 0.19 / σ(F): 1.36 / Phase error: 17.5 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1898	3840	1.5 %
R_work	0.1674	-	-
obs	0.1678	132374	99.67 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.702→45.047 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5175	0	630	785	6590

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6018
X-RAY DIFFRACTION	f_angle_d	1.125	8040
X-RAY DIFFRACTION	f_dihedral_angle_d	35.539	2883
X-RAY DIFFRACTION	f_chiral_restr	0.048	709
X-RAY DIFFRACTION	f_plane_restr	0.005	967

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 (%)
1.7023-1.7239	0.3215	138	0.2998	8915	X-RAY DIFFRACTION	95
1.7239-1.7465	0.2732	142	0.2694	9242	X-RAY DIFFRACTION	100
1.7465-1.7705	0.2531	137	0.2605	9327	X-RAY DIFFRACTION	100
1.7705-1.7958	0.262	143	0.2279	9301	X-RAY DIFFRACTION	100
1.7958-1.8226	0.2228	141	0.2114	9387	X-RAY DIFFRACTION	100
1.8226-1.8511	0.1824	144	0.2019	9316	X-RAY DIFFRACTION	100
1.8511-1.8814	0.2177	147	0.1865	9291	X-RAY DIFFRACTION	100
1.8814-1.9138	0.2113	141	0.1825	9330	X-RAY DIFFRACTION	100
1.9138-1.9486	0.1889	141	0.1689	9288	X-RAY DIFFRACTION	100
1.9486-1.9861	0.1789	144	0.1631	9378	X-RAY DIFFRACTION	100
1.9861-2.0267	0.1774	141	0.1597	9275	X-RAY DIFFRACTION	100
2.0267-2.0707	0.1947	144	0.1563	9298	X-RAY DIFFRACTION	100
2.0707-2.1189	0.1912	143	0.1625	9302	X-RAY DIFFRACTION	100
2.1189-2.1719	0.165	144	0.1548	9327	X-RAY DIFFRACTION	100
2.1719-2.2306	0.2107	143	0.1555	9284	X-RAY DIFFRACTION	100
2.2306-2.2963	0.1754	144	0.1601	9399	X-RAY DIFFRACTION	100
2.2963-2.3704	0.1904	141	0.1653	9291	X-RAY DIFFRACTION	100
2.3704-2.4551	0.1765	145	0.167	9320	X-RAY DIFFRACTION	100
2.4551-2.5534	0.2146	143	0.1679	9348	X-RAY DIFFRACTION	100
2.5534-2.6696	0.214	140	0.1643	9342	X-RAY DIFFRACTION	100
2.6696-2.8103	0.1909	144	0.1665	9303	X-RAY DIFFRACTION	100
2.8103-2.9863	0.2029	140	0.1711	9366	X-RAY DIFFRACTION	100
2.9863-3.2168	0.1977	142	0.1677	9344	X-RAY DIFFRACTION	100
3.2168-3.5405	0.1685	144	0.1545	9319	X-RAY DIFFRACTION	100
3.5405-4.0525	0.1981	141	0.1525	9313	X-RAY DIFFRACTION	100
4.0525-5.1046	0.1686	145	0.1399	9302	X-RAY DIFFRACTION	100
5.1046-45.0624	0.1608	138	0.1911	9322	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	0.5008	-0.0668	0.2749	0.7904	0.3036	0.2605	0.0163	-0.0181	0.0485	-0.1006	-0.0296	0.0485	-0.0199	-0.0915	-0.0218	0.1214	0.0062	-0.0114	0.1899	-0.0074	0.1751	148.3793	17.8056	35.757
2	1.6689	-0.2936	-1.5129	0.5298	0.2396	2.9618	-0.0383	0.1399	0.056	-0.1254	-0.0301	-0.0363	0.0121	-0.2129	0.0603	0.1625	-0.031	0.016	0.125	-0.0106	0.1765	160.6471	22.1026	35.3855
3	0.7203	-0.3134	-0.6476	2.5392	2.4771	3.9658	0.0274	0.0038	0.0573	-0.2016	0.0064	-0.1441	-0.1721	-0.0006	-0.0533	0.1597	0.012	0.0006	0.1319	0.0077	0.1912	163.2745	15.0384	38.9364
4	1.133	0.2907	1.0219	1.3621	1.1982	2.3243	0.0085	-0.0524	0.071	-0.041	0	-0.077	-0.1405	0.0376	0.0126	0.1499	0.0033	-0.0096	0.1312	0.0039	0.1739	161.8981	12.4697	45.4243
5	1.3916	-0.1938	1.8863	0.5914	0.0298	3.2584	0.1331	-0.0065	-0.0279	-0.0238	-0.0236	-0.0127	0.1376	-0.0339	-0.0969	0.1382	-0.0015	-0.0136	0.1504	-0.0027	0.1635	156.5243	6.9085	41.3308
6	1.1957	-0.7214	0.7459	0.7684	-0.7076	1.6348	0.1327	0.1356	0.0371	-0.0953	0.0192	-0.0881	0.0062	0.2549	-0.1089	0.1535	-0.0045	-0.0049	0.1908	0.0029	0.1956	124.2043	17.0403	20.5874
7	0.5533	-0.3456	-0.2274	1.193	0.4407	1.0133	0.101	0.0639	0.0567	-0.0661	-0.01	-0.1265	0.0156	0.0914	-0.1316	0.1601	0.0312	0.0016	0.2124	-0.0035	0.2265	127.6483	22.2854	20.8005
8	2.0511	-0.5309	-1.9222	0.7689	0.6017	3.0542	0.1136	0.1029	0.0962	-0.0646	-0.0199	-0.0529	-0.0448	-0.0101	-0.071	0.1453	0.0157	0.015	0.1395	0.0165	0.1881	119.2132	29.8903	20.1965
9	2.7526	1.1969	-3.5357	1.8787	-1.9708	5.9488	0.1663	0.1172	0.1216	-0.1272	-0.0953	0.0395	-0.2212	0.0634	-0.1249	0.1523	0.0281	-0.014	0.1759	0.018	0.1712	113.0437	28.0703	15.08
10	2.2167	0.2777	-1.7959	3.5225	-1.6558	2.7274	0.0262	-0.0688	-0.0738	0.1479	0.1489	0.3749	-0.196	-0.2254	-0.1086	0.12	0.0201	-0.0391	0.134	-0.0376	0.1685	108.9533	19.1865	21.8986
11	0.845	-0.3703	0.5301	2.1595	-1.6446	2.6517	0.0846	0.0506	-0.0174	-0.0029	0.0095	0.0778	-0.1877	-0.0526	-0.0603	0.1837	0.0394	-0.0429	0.1713	-0.0004	0.1712	113.6058	18.9205	14.9085
12	1.8359	-0.2365	1.8446	0.9058	-0.528	3.4817	0.1097	0.0247	-0.0196	-0.1384	-0.0091	0.0293	-0.0834	-0.1843	-0.1377	0.1615	0.0644	-0.0228	0.1528	-0.0229	0.1591	115.985	16.4931	10.5318

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 13 THROUGH 146 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 147 THROUGH 187 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 188 THROUGH 250 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 251 THROUGH 278 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 279 THROUGH 324 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 16 THROUGH 42 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 43 THROUGH 123 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 124 THROUGH 187 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 188 THROUGH 230 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 231 THROUGH 250 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 251 THROUGH 297 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 298 THROUGH 324 )

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