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- PDB-6mgb: Thermosulfurimonas dismutans KpsC, beta Kdo 2,4 transferase -

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Basic information

Entry
Database: PDB / ID: 6mgb
TitleThermosulfurimonas dismutans KpsC, beta Kdo 2,4 transferase
ComponentsCapsular polysaccharide export system protein KpsC
KeywordsTRANSFERASE / glycosyltransferase / cytosine monophosphate
Function / homologyCapsule polysaccharide biosynthesis / Capsule polysaccharide biosynthesis protein / polysaccharide transport / polysaccharide biosynthetic process / CYTIDINE-5'-MONOPHOSPHATE / Capsular polysaccharide export system protein KpsC
Function and homology information
Biological speciesThermosulfurimonas dismutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDoyle, L. / Mallette, E. / Kimber, M.S. / Whitfield, C.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)04045-2015 Canada
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: Biosynthesis of a conserved glycolipid anchor for Gram-negative bacterial capsules.
Authors: Doyle, L. / Ovchinnikova, O.G. / Myler, K. / Mallette, E. / Huang, B.S. / Lowary, T.L. / Kimber, M.S. / Whitfield, C.
History
DepositionSep 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2May 8, 2019Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3May 15, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4May 29, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsular polysaccharide export system protein KpsC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6974
Polymers37,3141
Non-polymers3833
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-25 kcal/mol
Surface area15460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.020, 65.540, 121.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Capsular polysaccharide export system protein KpsC / KpsC-N beta(2 / 4) Kdo-transferase


Mass: 37314.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosulfurimonas dismutans (bacteria)
Gene: TDIS_2046 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A179D1D1
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE / Cytidine monophosphate


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M magnesium chloride hexahydrate, 0.1 M Tris-HCl, pH 7.0, 10% v/v PEG8000, 10 mg/mL protein with 1 mM CMP, 50 mM L-Arg

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 27, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 37637 / % possible obs: 99.9 % / Redundancy: 6.2 % / Rsym value: 0.123 / Net I/σ(I): 7.9
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.74 / Num. unique obs: 2738 / CC1/2: 0.73 / Rsym value: 0.84 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→46.23 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.32
RfactorNum. reflection% reflection
Rfree0.2128 1414 3.76 %
Rwork0.1827 --
obs0.1838 37635 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→46.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2601 0 23 271 2895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022785
X-RAY DIFFRACTIONf_angle_d0.5423783
X-RAY DIFFRACTIONf_dihedral_angle_d16.331685
X-RAY DIFFRACTIONf_chiral_restr0.044397
X-RAY DIFFRACTIONf_plane_restr0.003487
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.86430.26761390.26443561X-RAY DIFFRACTION100
1.8643-1.9390.27371390.23623567X-RAY DIFFRACTION100
1.939-2.02720.26781400.2143578X-RAY DIFFRACTION100
2.0272-2.13410.2391390.19663564X-RAY DIFFRACTION100
2.1341-2.26780.1951410.1813612X-RAY DIFFRACTION100
2.2678-2.44290.22041400.18883588X-RAY DIFFRACTION100
2.4429-2.68870.22791410.19143612X-RAY DIFFRACTION100
2.6887-3.07770.24921420.19273636X-RAY DIFFRACTION100
3.0777-3.87730.20711440.17223690X-RAY DIFFRACTION100
3.8773-46.24560.1781490.16443813X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 66.1441 Å / Origin y: 67.3301 Å / Origin z: 148.8584 Å
111213212223313233
T0.2253 Å20.0067 Å20.0033 Å2-0.25 Å2-0.0093 Å2--0.2473 Å2
L0.2669 °2-0.0816 °20.3109 °2-0.6487 °2-0.0664 °2--0.6494 °2
S0.0429 Å °-0.0054 Å °-0.0617 Å °0.0117 Å °-0.0429 Å °-0.0006 Å °-0.0197 Å °-0.061 Å °-0.0004 Å °
Refinement TLS groupSelection details: all

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