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- PDB-8fux: KpsC D160C ternary complex -

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Basic information

Entry
Database: PDB / ID: 8fux
TitleKpsC D160C ternary complex
ComponentsCapsule polysaccharide export protein KpsC
KeywordsTRANSFERASE / glycosyltransferase / retaining
Function / homology
Function and homology information


polysaccharide transport / polysaccharide biosynthetic process
Similarity search - Function
Capsule polysaccharide biosynthesis / Capsule polysaccharide biosynthesis protein
Similarity search - Domain/homology
CYTIDINE-5'-MONOPHOSPHATE / 3-deoxy-beta-D-manno-oct-2-ulopyranosonic acid / 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid / PHOSPHATE ION / N-(8-hydroxyoctyl)-4-methoxybenzamide / Capsule polysaccharide export protein KpsC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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
B: Capsule polysaccharide export protein KpsC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,43414
Polymers72,9572
Non-polymers2,47712
Water16,880937
1
A: Capsule polysaccharide export protein KpsC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8317
Polymers36,4791
Non-polymers1,3536
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Capsule polysaccharide export protein KpsC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6037
Polymers36,4791
Non-polymers1,1246
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.540, 80.300, 65.980
Angle α, β, γ (deg.)90.000, 103.039, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Capsule polysaccharide export protein KpsC


Mass: 36478.633 Da / Num. of mol.: 2 / Mutation: D160C
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
#5: 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
IdentifierTypeProgram
DKdopaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-KdopIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
KdoSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 947 molecules

#2: Chemical
ChemComp-KD3 / 3-deoxy-beta-D-manno-oct-2-ulopyranosonic acid


Mass: 238.192 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H14O8 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-PXV / N-(8-hydroxyoctyl)-4-methoxybenzamide


Mass: 279.375 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25NO3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 937 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.07 Å3/Da / Density % sol: 40.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 25 % (v/v) PEG 3350 and 0.1 M Bis-Tris, pH 5.5

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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: 1.2→48.43 Å / Num. obs: 184570 / % possible obs: 99.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 12.94 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.078 / Net I/σ(I): 9
Reflection shellResolution: 1.2→1.25 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.39 / Num. unique obs: 21213 / CC1/2: 0.521 / Rrim(I) all: 1.104 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→48.43 Å / SU ML: 0.1339 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.5116
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1568 9229 5 %
Rwork0.1238 175341 -
obs0.1254 184570 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.12 Å2
Refinement stepCycle: LAST / Resolution: 1.2→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4980 0 158 937 6075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0215861
X-RAY DIFFRACTIONf_angle_d1.58468106
X-RAY DIFFRACTIONf_chiral_restr0.1203906
X-RAY DIFFRACTIONf_plane_restr0.01521047
X-RAY DIFFRACTIONf_dihedral_angle_d15.30232239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.210.27663070.23915841X-RAY DIFFRACTION99.76
1.21-1.230.27053060.23765811X-RAY DIFFRACTION99.95
1.23-1.240.28953070.22915840X-RAY DIFFRACTION99.79
1.24-1.260.25623060.22165801X-RAY DIFFRACTION99.89
1.26-1.280.2983100.23835885X-RAY DIFFRACTION99.94
1.28-1.290.26133070.22285835X-RAY DIFFRACTION99.81
1.29-1.310.26643040.21055791X-RAY DIFFRACTION99.67
1.31-1.330.21813100.19065885X-RAY DIFFRACTION99.9
1.33-1.350.21593050.17135782X-RAY DIFFRACTION99.82
1.35-1.370.21573090.15255876X-RAY DIFFRACTION99.73
1.37-1.40.19383060.14035826X-RAY DIFFRACTION99.85
1.4-1.420.18283080.12875853X-RAY DIFFRACTION99.95
1.42-1.450.18843060.12715808X-RAY DIFFRACTION99.97
1.45-1.480.15763080.11935857X-RAY DIFFRACTION99.85
1.48-1.510.17763090.1185862X-RAY DIFFRACTION99.85
1.51-1.550.16893080.12255858X-RAY DIFFRACTION99.89
1.55-1.590.17693070.11475824X-RAY DIFFRACTION99.82
1.59-1.630.15843090.09825867X-RAY DIFFRACTION99.82
1.63-1.680.13933090.09525878X-RAY DIFFRACTION99.89
1.68-1.730.13883070.09585833X-RAY DIFFRACTION99.79
1.73-1.790.14413060.09685811X-RAY DIFFRACTION99.79
1.79-1.860.14783080.0985864X-RAY DIFFRACTION99.71
1.86-1.950.13833100.09925872X-RAY DIFFRACTION99.58
1.95-2.050.14393050.10355804X-RAY DIFFRACTION99.5
2.05-2.180.14083060.10365809X-RAY DIFFRACTION98.74
2.18-2.350.13633080.10675858X-RAY DIFFRACTION99.39
2.35-2.590.14953060.11255809X-RAY DIFFRACTION98.98
2.59-2.960.15063100.12525895X-RAY DIFFRACTION99.74
2.96-3.730.13453090.12025861X-RAY DIFFRACTION99.07
3.73-48.430.1343130.12715945X-RAY DIFFRACTION99.14

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