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- PDB-6yuq: Capsule O-acetyltransferase of Neisseria meningitidis serogroup A... -

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Basic information

Entry
Database: PDB / ID: 6yuq
TitleCapsule O-acetyltransferase of Neisseria meningitidis serogroup A in complex with polysaccharide
ComponentsSacC
KeywordsTRANSFERASE / O-acetyltransferase / a/b hydrolase fold / serine transferase / catalytic triad
Function / homologyUncharacterised protein family UPF0227/Esterase YqiA / Uncharacterised protein family (UPF0227) / Alpha/Beta hydrolase fold / 2-acetamido-2-deoxy-alpha-D-mannopyranose / Chem-BMX / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / SacC
Function and homology information
Biological speciesNeisseria meningitidis serogroup A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsCramer, J.T. / Fiebig, T. / Fedorov, R. / Muehlenhoff, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)262794208 Germany
German Research Foundation (DFG)412824531 Germany
CitationJournal: Nat Commun / Year: 2020
Title: Structural and mechanistic basis of capsule O-acetylation in Neisseria meningitidis serogroup A.
Authors: Fiebig, T. / Cramer, J.T. / Bethe, A. / Baruch, P. / Curth, U. / Fuhring, J.I. / Buettner, F.F.R. / Vogel, U. / Schubert, M. / Fedorov, R. / Muhlenhoff, M.
History
DepositionApr 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SacC
B: SacC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,26311
Polymers58,7492
Non-polymers1,5149
Water84747
1
A: SacC
B: SacC
hetero molecules

A: SacC
B: SacC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,52622
Polymers117,4984
Non-polymers3,02818
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area7960 Å2
ΔGint-50 kcal/mol
Surface area38130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.483, 137.483, 70.253
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein SacC


Mass: 29374.439 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup A (bacteria)
Gene: sacC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O68216

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Sugars , 2 types, 4 molecules

#5: Sugar ChemComp-BMX / 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-mannopyranose / 2-(ACETYLAMINO)-2-DEOXY-6-O-PHOSPHONO-ALPHA-D-MANNOPYRANOSE / N-acetyl-6-O-phosphono-alpha-D-mannosamine / 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-mannose / 2-acetamido-2-deoxy-6-O-phosphono-D-mannose / 2-acetamido-2-deoxy-6-O-phosphono-mannose


Type: D-saccharide, alpha linking / Mass: 301.188 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H16NO9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-ManpNAc6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#6: Sugar ChemComp-BM3 / 2-acetamido-2-deoxy-alpha-D-mannopyranose / N-acetyl-alpha-D-mannosamine / 2-acetamido-2-deoxy-alpha-D-mannose / 2-acetamido-2-deoxy-D-mannose / 2-acetamido-2-deoxy-mannose / 2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-MANNOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-mannopyranosamineCOMMON NAMEGMML 1.0
a-D-ManpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 52 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.83 Å3/Da / Density % sol: 56.47 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: Native wild type CsaC crystallized in sitting drop setups at concentrations of approx. 18mg/ml. Fine screens around initial screening conditions resulted in many isomorphous crystals. Mother ...Details: Native wild type CsaC crystallized in sitting drop setups at concentrations of approx. 18mg/ml. Fine screens around initial screening conditions resulted in many isomorphous crystals. Mother liquor contained 50mM HEPES pH 7.0, 100 mM HEPES pH 7.6, 100mM NaCl, 5mM MgCl2, 1mM EDTA, and 31-42% PEG200. Good quality crystals grew at 4, 12, and 18C.
PH range: 7.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.95→48.62 Å / Num. obs: 49502 / % possible obs: 99.9 % / Redundancy: 26.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.012 / Rrim(I) all: 0.06 / Net I/σ(I): 25.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.95-2.0225.62.8181.248470.7740.5652.87499.9
2.02-2.127.31.9471.848750.8660.3781.984100
2.1-2.22.91.2052.948980.9420.2351.228100
2.2-2.31270.7984.548940.9710.1560.81399.9
2.31-2.4627.20.4427.949020.9920.0860.45100
2.46-2.6527.50.2731349090.9960.0530.278100
2.65-2.9126.90.14823.349510.9990.0290.15199.9
2.91-3.3325.60.08342.549650.9990.0170.08599.9
3.33-4.224.10.0567.5501610.010.05199.9
4.2-48.6223.70.0480.552450.9980.0080.04199.9

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHENIXmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YUO

6yuo


Resolution: 1.95→46.27 Å / SU ML: 0.2771 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.6893
RfactorNum. reflection% reflection
Rfree0.2207 2475 5 %
Rwork0.2095 --
obs0.21 49462 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 71.33 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3898 0 92 47 4037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00564070
X-RAY DIFFRACTIONf_angle_d0.75365518
X-RAY DIFFRACTIONf_chiral_restr0.0523634
X-RAY DIFFRACTIONf_plane_restr0.0036683
X-RAY DIFFRACTIONf_dihedral_angle_d18.65731451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.990.42571350.38922556X-RAY DIFFRACTION99.89
1.99-2.030.35911360.35232572X-RAY DIFFRACTION99.74
2.03-2.070.36071360.32982576X-RAY DIFFRACTION99.85
2.07-2.120.34961340.30062566X-RAY DIFFRACTION100
2.12-2.170.31981360.29192569X-RAY DIFFRACTION99.93
2.17-2.230.29581340.26852573X-RAY DIFFRACTION99.96
2.23-2.30.27771380.26882589X-RAY DIFFRACTION99.93
2.3-2.370.3031370.25742599X-RAY DIFFRACTION99.89
2.37-2.460.27591340.25652569X-RAY DIFFRACTION99.74
2.46-2.560.27361370.26052586X-RAY DIFFRACTION99.93
2.56-2.670.33131360.25692600X-RAY DIFFRACTION99.82
2.67-2.810.27241390.25952615X-RAY DIFFRACTION99.93
2.81-2.990.25041370.25242591X-RAY DIFFRACTION99.74
2.99-3.220.30491380.26142633X-RAY DIFFRACTION99.93
3.22-3.540.22081380.2362626X-RAY DIFFRACTION99.86
3.54-4.060.18181410.19482656X-RAY DIFFRACTION99.96
4.06-5.110.1991400.16512678X-RAY DIFFRACTION99.96
5.11-46.270.17721490.17492833X-RAY DIFFRACTION99.87
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)
15.25281784017-0.02146390075751.435333172583.105876358720.4163050565964.2815573614-0.08077584460280.607793412867-0.185272893419-0.2665041095420.211205946926-0.1686547588510.08536253479210.526052425546-0.1094347346860.431147250006-0.0383903206750.01193308550450.434130478689-0.04446547552320.33965301191-6.6631366186239.8526609007-29.4478050951
22.986769516471.08614677782-1.668604748673.08826241862-1.598424228954.10746816191-0.0834255272161-0.271833686261-0.3498488428080.169877097435-0.130594479159-0.2305817687140.5111800275050.3065367631950.2087243117960.4900681379550.0367205650154-0.06178457283520.435509048905-0.06918402745080.445063516037-1.2634356778431.12190247953.25547887035
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 1 - 245 / Label seq-ID: 1 - 245

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain A and resseq 1:245)AA
22(chain B and resseq 1:245)BE

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