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- PDB-8fuw: KpsC D160N Kdo adduct -

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Basic information

Entry
Database: PDB / ID: 8fuw
TitleKpsC D160N Kdo adduct
ComponentsCapsule polysaccharide export protein KpsC
KeywordsTRANSFERASE / glycosyltransferase / retaining
Function / homologyCapsule polysaccharide biosynthesis / Capsule polysaccharide biosynthesis protein / polysaccharide transport / polysaccharide biosynthetic process / CYTIDINE-5'-MONOPHOSPHATE / 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid / Capsule polysaccharide export protein KpsC
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKimber, M.S. / Doyle, L. / Whitfield, C.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)400427 Canada
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Mechanism and linkage specificities of the dual retaining beta-Kdo glycosyltransferase modules of KpsC from bacterial capsule biosynthesis.
Authors: Doyle, L. / Ovchinnikova, O.G. / Huang, B.S. / Forrester, T.J.B. / Lowary, T.L. / Kimber, M.S. / Whitfield, C.
History
DepositionJan 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2May 3, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsule polysaccharide export protein KpsC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3255
Polymers36,4901
Non-polymers8354
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.380, 64.380, 139.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Capsule polysaccharide export protein KpsC


Mass: 36489.590 Da / Num. of mol.: 1 / Mutation: D160N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: kpsC / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2Z2W8
#2: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-KDO / 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid / 3-deoxy-d-manno-oct-2-ulopyranosonic acid / 2-keto-3-deoxy-D-mannooctanoic acid / 3-deoxy-alpha-D-manno-oct-2-ulosonic acid / 3-deoxy-D-manno-oct-2-ulosonic acid / 3-deoxy-manno-oct-2-ulosonic acid


Type: D-saccharide, alpha linking / Mass: 238.192 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H14O8 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DKdopaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-KdopIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
KdoSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M lithium sulfate, 29 % (v/v) PEG 3350 and 0.1 M Bis-Tris, pH 5.5 and 2 mM strontium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.9→46.4 Å / Num. obs: 27085 / % possible obs: 99.9 % / Redundancy: 9.6 % / Biso Wilson estimate: 42.94 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.084 / Net I/σ(I): 12.74
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 1.09 / Num. unique obs: 2008 / CC1/2: 0.542 / Rrim(I) all: 2.66 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→46.4 Å / SU ML: 0.2316 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5086
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2257 1353 5 %
Rwork0.1905 25717 -
obs0.1923 27070 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.53 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2449 0 53 104 2606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00992618
X-RAY DIFFRACTIONf_angle_d0.9643585
X-RAY DIFFRACTIONf_chiral_restr0.056407
X-RAY DIFFRACTIONf_plane_restr0.0085457
X-RAY DIFFRACTIONf_dihedral_angle_d14.6361952
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.970.4141310.37442522X-RAY DIFFRACTION99.62
1.97-2.050.36081330.29532511X-RAY DIFFRACTION100
2.05-2.140.32211340.2692543X-RAY DIFFRACTION100
2.14-2.250.26951330.24652542X-RAY DIFFRACTION100
2.25-2.390.23911340.19762542X-RAY DIFFRACTION99.96
2.39-2.580.24671350.20292558X-RAY DIFFRACTION99.89
2.58-2.840.24851350.20742559X-RAY DIFFRACTION100
2.84-3.250.26031360.21482585X-RAY DIFFRACTION100
3.25-4.090.21261360.17462594X-RAY DIFFRACTION99.78
4.09-46.40.18591460.15952761X-RAY DIFFRACTION99.93
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)
16.335321676680.332642936746-0.6244916654240.797510897306-0.9166915084182.498751826560.564025821725-0.833707403543-0.628841060840.479423922072-0.262711416056-0.4534525516080.4996995298860.210065174578-0.23414192650.742277313882-0.274540115732-0.2615001007360.452266061550.105612872050.77847901368937.8751985951-15.693920905412.0589108294
22.900743169990.5620113559720.9499356712063.494416134841.246158309873.024549906150.067977640944-0.3927512103480.05357081186760.148086698234-0.09542590458190.157639194554-0.0189872675093-0.4336433604880.01981997016350.604814990372-0.251782005259-0.0535258278990.366241375010.05942788329420.58215828961121.1066700881-3.659734238436.45346967289
32.41943024402-0.05030398684510.8188695399052.817659790681.067575170071.96026335296-0.0221470192625-0.5285816399060.2976585693120.0656348015217-0.06468122916820.303678752197-0.181264577029-0.5405247852970.1078336505230.55796457926-0.24462683802-0.05954485813090.425058213417-0.001904090028280.63143210411619.74232062092.124558875158.45889557654
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 88 )1 - 881 - 88
22chain 'A' and (resid 89 through 169 )89 - 16989 - 165
33chain 'A' and (resid 170 through 320 )170 - 320166 - 316

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