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- PDB-4v3g: Crystal structure of CymA from Klebsiella oxytoca -

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Basic information

Entry
Database: PDB / ID: 4v3g
TitleCrystal structure of CymA from Klebsiella oxytoca
ComponentsCYMA PROTEIN
KeywordsTRANSPORT 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 / CymA protein
Function and homology information
Biological speciesKLEBSIELLA OXYTOCA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.513 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
DepositionOct 18, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references / 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
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. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" 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 PROTEIN
B: CYMA PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,06312
Polymers79,9992
Non-polymers3,06410
Water93752
1
A: CYMA PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,75710
Polymers39,9991
Non-polymers2,7589
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CYMA PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3062
Polymers39,9991
Non-polymers3061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.594, 105.226, 111.815
Angle α, β, γ (deg.)90.00, 97.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CYMA PROTEIN / CYMA


Mass: 39999.426 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: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE (C8E): MOST DETERGENT MOLECULES ARE ONLY PARTIALLY ORDERED
Sequence detailsMETHIONINES REPLACED BY SELENO-METHIONINES

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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: 3.2 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growpH: 8.5
Details: MOLECULAR DIMENSIONS MORPHEUS 1/35 OPTIMIZED, pH 8.5

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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: Jun 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 32944 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Biso Wilson estimate: 59.32 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 33.5
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.513→48.998 Å / SU ML: 0.33 / σ(F): 0 / Phase error: 27.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2525 1989 6.1 %
Rwork0.1922 --
obs0.1958 32780 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.513→48.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5450 0 122 52 5624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095743
X-RAY DIFFRACTIONf_angle_d1.1567704
X-RAY DIFFRACTIONf_dihedral_angle_d20.6062145
X-RAY DIFFRACTIONf_chiral_restr0.039729
X-RAY DIFFRACTIONf_plane_restr0.0041005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5127-2.57550.29011280.2411996X-RAY DIFFRACTION91
2.5755-2.64520.30881480.22942199X-RAY DIFFRACTION98
2.6452-2.7230.26691440.22922168X-RAY DIFFRACTION98
2.723-2.81090.2781430.21152199X-RAY DIFFRACTION99
2.8109-2.91130.28011470.21862168X-RAY DIFFRACTION98
2.9113-3.02790.32621390.22022232X-RAY DIFFRACTION99
3.0279-3.16570.24081400.20752179X-RAY DIFFRACTION99
3.1657-3.33250.25381420.19522219X-RAY DIFFRACTION99
3.3325-3.54130.23651410.18162239X-RAY DIFFRACTION99
3.5413-3.81460.22591410.18822218X-RAY DIFFRACTION100
3.8146-4.19830.27261420.18692233X-RAY DIFFRACTION99
4.1983-4.80540.22311440.15892227X-RAY DIFFRACTION99
4.8054-6.05250.22661410.18022254X-RAY DIFFRACTION100
6.0525-49.00760.27581490.21142260X-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)
11.1105-0.1247-0.44690.126-0.18650.76180.0560.3459-0.1842-0.51080.2636-0.3541-0.19860.5154-0.33910.4490.0133-0.04620.6285-0.07560.54180.782210.389616.8052
20.9876-0.289-0.14881.41570.42610.7901-0.1407-0.1368-0.05830.29720.0806-0.00940.05860.0240.05510.38070.0242-0.04630.4082-0.01840.4503-0.6502-10.215914.543
30.27710.49840.09970.89890.30451.4202-0.641-0.4577-0.29721.03340.28160.13890.6947-0.16980.24961.02160.00980.14480.9256-0.08860.8364-15.67012.782742.9289
41.538-0.43-0.47551.3278-0.17581.81910.0573-0.1791-0.02980.4733-0.01070.1642-0.31710.0488-0.00510.5767-0.03570.07410.4589-0.02350.4436-20.32117.539940.7189
51.48080.0229-0.60112.738-0.6291.31810.2069-0.09550.24830.3448-0.10590.0194-0.56320.0224-0.12470.6170.00720.0810.4791-0.04510.4546-28.721724.191336.8673
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID -14 THROUGH 21 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 22 THROUGH 324 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID -14 THROUGH 21 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 22 THROUGH 297 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 298 THROUGH 324 )

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