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- PDB-4d5d: Crystal structure of CymA from Klebsiella oxytoca -

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Basic information

Entry
Database: PDB / ID: 4d5d
TitleCrystal structure of CymA from Klebsiella oxytoca
ComponentsCYMA
KeywordsSTRUCTURAL PROTEIN / OUTER MEMBRANE CHANNEL CYCLODEXTRIN TRANSPORT BETA BARREL MONOMER
Function / homologyCyclodextrin porin CymA / Putative cyclodextrin porin / import into cell / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / beta-cyclodextrin / alpha-cyclodextrin / CymA protein
Function and homology information
Biological speciesKLEBSIELLA OXYTOCA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.902 Å
Authorsvan den Berg, B. / Bhamidimarri, S.P. / Kleinekathoefer, U. / Winterhalter, M.
CitationJournal: 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
DepositionNov 3, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Source and taxonomy
Revision 1.2Jun 24, 2015Group: Database references
Revision 1.3Feb 21, 2018Group: 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 2.0Jul 29, 2020Group: 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 / 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_close_contact / 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.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _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_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: 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 ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 14-STRANDED BARREL THIS IS REPRESENTED BY A 15-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYMA
B: CYMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,22826
Polymers79,8112
Non-polymers10,41624
Water10,377576
1
A: CYMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,11413
Polymers39,9061
Non-polymers5,20812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CYMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,11413
Polymers39,9061
Non-polymers5,20812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)140.160, 77.991, 109.927
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2081-

HOH

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Components

#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.: 2
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: alpha-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,6,6/[a2122h-1a_1-5]/1-1-1-1-1-1/a1-f4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
#3: Polysaccharide Cycloheptakis-(1-4)-(alpha-D-glucopyranose) / beta-cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1153.001 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: beta-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,7,7/[a2122h-1a_1-5]/1-1-1-1-1-1-1/a1-g4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
#4: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 576 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 68 % / Description: NONE
Crystal growpH: 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.9→47 Å / Num. obs: 94765 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Biso Wilson estimate: 28.75 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 9 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4V3G

4v3g


Resolution: 1.902→47.1 Å / SU ML: 0.17 / σ(F): 1.35 / Phase error: 18.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1976 3757 2.2 %
Rwork0.1786 --
obs0.179 93335 95.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.902→47.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5173 0 533 576 6282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075892
X-RAY DIFFRACTIONf_angle_d1.1577910
X-RAY DIFFRACTIONf_dihedral_angle_d33.9252834
X-RAY DIFFRACTIONf_chiral_restr0.047696
X-RAY DIFFRACTIONf_plane_restr0.005958
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9015-1.92560.2796850.25094039X-RAY DIFFRACTION61
1.9256-1.95090.22331390.23446242X-RAY DIFFRACTION95
1.9509-1.97760.25121340.21176287X-RAY DIFFRACTION95
1.9776-2.00590.18881410.2066419X-RAY DIFFRACTION95
2.0059-2.03580.23031370.19516220X-RAY DIFFRACTION95
2.0358-2.06770.21941360.19566302X-RAY DIFFRACTION95
2.0677-2.10160.21031380.19156375X-RAY DIFFRACTION96
2.1016-2.13780.20471450.18486358X-RAY DIFFRACTION96
2.1378-2.17670.1731390.17746378X-RAY DIFFRACTION96
2.1767-2.21850.231430.1756365X-RAY DIFFRACTION96
2.2185-2.26380.2251370.18246377X-RAY DIFFRACTION96
2.2638-2.3130.21561400.18236381X-RAY DIFFRACTION96
2.313-2.36680.21511370.17986425X-RAY DIFFRACTION96
2.3668-2.4260.21271440.17236404X-RAY DIFFRACTION97
2.426-2.49160.18911410.1776453X-RAY DIFFRACTION97
2.4916-2.56490.21061380.1726387X-RAY DIFFRACTION97
2.5649-2.64770.20131430.16446456X-RAY DIFFRACTION97
2.6477-2.74230.20791420.16576513X-RAY DIFFRACTION98
2.7423-2.85210.20661430.16776479X-RAY DIFFRACTION98
2.8521-2.98190.18691450.186514X-RAY DIFFRACTION98
2.9819-3.13910.19671430.17026525X-RAY DIFFRACTION98
3.1391-3.33570.15051440.16456511X-RAY DIFFRACTION98
3.3357-3.59320.19371420.16916534X-RAY DIFFRACTION99
3.5932-3.95460.18481440.16986574X-RAY DIFFRACTION99
3.9546-4.52650.17551460.1636599X-RAY DIFFRACTION99
4.5265-5.70130.1691460.17076579X-RAY DIFFRACTION99
5.7013-47.11440.28241450.22996588X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.74190.13390.36510.14540.16260.23750.0012-0.05110.1150.1325-0.05890.0797-0.1337-0.1282-0.03140.27980.0199-0.01260.3006-0.01620.27277.607413.915833.7311
20.60780.02130.10550.82540.44410.2409-0.0151-0.12380.06-0.0635-0.07170.03940.0257-0.0847-0.06090.17210.0063-0.01870.2902-0.02620.24426.654618.256235.746
31.00650.0008-0.16250.4465-0.03790.9224-0.08230.02230.0327-0.0439-0.0296-0.00980.0372-0.1311-0.02750.2235-0.00730.02110.1776-0.02510.245117.130822.348336.1084
40.7539-0.0231-0.24571.22270.61421.40890.0196-0.04120.0876-0.10450.0701-0.1638-0.12980.0582-0.06350.20.018-0.01630.1899-0.00770.2522.500515.025938.4899
50.524-0.29910.08870.6072-0.0760.3420.0663-0.1138-0.01190.048-0.0206-0.0710.048-0.0325-0.0430.23220.0059-0.02680.1986-0.01430.225117.71199.223342.6835
60.8345-0.47770.26670.295-0.30181.02970.04230.08050.1475-0.1231-0.0024-0.0369-0.08780.12220.00920.27280.0077-0.01970.2496-0.01410.2882-16.390417.10420.2541
70.6684-0.3641-0.08120.6758-0.34090.27580.07110.08910.0593-0.02090.0238-0.05980.00330.0902-0.04520.18010.04680.00050.2423-0.01470.2576-12.605720.509120.4557
80.6326-0.1648-0.37690.52440.20551.03130.06950.060.1090.0161-0.0006-0.10040.07730.0286-0.06660.24410.00330.02150.21360.00540.2569-18.14429.564821.3566
91.1050.1165-0.93030.74850.28040.93590.121-0.0230.1104-0.0886-0.05480.0512-0.08120.0823-0.03840.24820.03650.01380.27780.05660.2706-25.578729.086617.8363
101.35480.0206-0.7581.3929-0.34391.83190.09490.02740.07-0.0726-0.0880.105-0.09970.0519-0.08960.2210.0324-0.01430.26780.00760.2534-28.429524.157216.0155
110.6358-0.27170.07270.9676-0.37630.43720.08140.0965-0.01260.0254-0.00740.0757-0.1930.0243-0.08250.25160.0088-0.05710.2370.01870.2164-26.859719.278214.4493
120.94840.0690.49890.5893-0.10940.92210.13510.101-0.0778-0.1075-0.02760.1101-0.0088-0.0938-0.05180.24580.0501-0.01840.2433-0.01410.2408-24.625216.64510.3977
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 14 THROUGH 42 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 43 THROUGH 123 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 124 THROUGH 187 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 188 THROUGH 250 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 251 THROUGH 324 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 16 THROUGH 42 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 43 THROUGH 103 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 104 THROUGH 165 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 166 THROUGH 206 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 207 THROUGH 250 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 251 THROUGH 297 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 298 THROUGH 324 )

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