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

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Basic information

Entry
Database: PDB / ID: 6yuo
TitleCapsule O-acetyltransferase of Neisseria meningitidis serogroup A in complex with caged Gadolinium
ComponentsSacC
KeywordsTRANSFERASE / O-acetyltransferase / a/b hydrolase fold / serine transferase / catalytic triad
Function / homologyUncharacterised protein family (UPF0227) / Alpha/Beta hydrolase fold / GADOLINIUM ION / DI(HYDROXYETHYL)ETHER / SacC
Function and homology information
Biological speciesNeisseria meningitidis serogroup A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)59,3028
Polymers58,7492
Non-polymers5546
Water1,44180
1
A: SacC
B: SacC
hetero molecules

A: SacC
B: SacC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,60516
Polymers117,4984
Non-polymers1,10712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)132.930, 132.930, 69.270
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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Non-polymers , 5 types, 86 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GD3 / GADOLINIUM ION


Mass: 157.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Gd / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: Native wild type CsaC crystallized in sitting drop setups at concentrations of 18 mg/ml. Fine screens around initial screening conditions resulted in many isomorphous crystals. Mother liquor ...Details: Native wild type CsaC crystallized in sitting drop setups at concentrations of 18 mg/ml. Fine screens around initial screening conditions resulted in many isomorphous crystals. Mother liquor contained 50 mM HEPES pH 7.0, 100 mM HEPES pH 7.6, 100 mM NaCl, 5 mM MgCl2, 1 mM EDTA, and 31-42% PEG200.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.71177 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.71177 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 28553 / % possible obs: 89.3 % / Redundancy: 24.5 % / Biso Wilson estimate: 52.002 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.017 / Rrim(I) all: 0.087 / Net I/σ(I): 26.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.2-2.2825.50.9523.927990.8970.1890.97289.6
2.28-2.3724.80.7185.227460.9380.1440.73387.3
2.37-2.4825.20.517.627760.9650.1020.52188
2.48-2.6125.10.3841028630.9820.0770.39291.3
2.61-2.7724.60.2621427660.9910.0530.26887
2.77-2.9925.40.1721.928480.9960.0340.17490
2.99-3.2924.30.10932.329050.9980.0220.11191.4
3.29-3.7623.80.07445.428380.9990.0150.07688.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.18refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→19.87 Å / SU ML: 0.1995 / Cross valid method: FREE R-VALUE / Phase error: 22.3343
RfactorNum. reflection% reflection
Rfree0.2187 1427 5 %
Rwork0.1824 --
obs0.1843 28548 89.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 55.05 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3857 0 15 80 3952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00293946
X-RAY DIFFRACTIONf_angle_d0.60575337
X-RAY DIFFRACTIONf_chiral_restr0.0435607
X-RAY DIFFRACTIONf_plane_restr0.003666
X-RAY DIFFRACTIONf_dihedral_angle_d15.5561433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.280.29081400.23162650X-RAY DIFFRACTION89.45
2.28-2.370.29411370.22382604X-RAY DIFFRACTION87.35
2.37-2.480.24491390.20642639X-RAY DIFFRACTION88.16
2.48-2.610.25251420.20132720X-RAY DIFFRACTION91.38
2.61-2.770.24321390.20942655X-RAY DIFFRACTION87.72
2.77-2.980.29941430.2032701X-RAY DIFFRACTION90.23
2.98-3.280.23131450.19342763X-RAY DIFFRACTION91.53
3.28-3.750.21241410.17772684X-RAY DIFFRACTION88.09
3.76-4.720.18061470.15242780X-RAY DIFFRACTION90.23
4.72-19.870.20151540.17922925X-RAY DIFFRACTION90.61
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)
17.928757236050.469207268170.4012349198038.1461380175-0.3496414774612.008542590560.0121802172051.250452150240.4315569712810.237970054643-0.3683909472060.92007208683-1.11213203986-2.3685839210.3469945233070.4848600833740.1423824949510.06481967087660.7964368579840.06359375741660.66268520871252.690785403738.480533216810.6976451596
24.00257511280.974665621793-2.185586115039.38941600093-2.337475338047.26860916963-0.004943966141570.1428046377420.398235616971-0.186708344030.03883635317160.169908718465-0.660709716874-0.392161748833-0.05936732188510.3142144431680.0413217936636-0.05760685890340.337501061624-0.01068494274640.25725658067761.945029747433.55561717285.85190053905
35.045828033744.03870185777-0.6030797014232.04995748616-2.222373971728.70878214483-0.01636915826341.433947890230.505295811682-0.3719993449090.2740011517911.036168539330.0146481411922-1.68589705801-0.4215241476460.3966811352860.00130698487928-0.05460804726450.812944850026-0.002776904316790.54427406841755.973727640426.1280527622.75736540359
47.58742091452-2.612110521430.8441462008042.09162612406-7.175042088522.11078479413-0.0290117672096-0.5561901397830.9477892662430.878435281246-0.0440607314517-0.0128999298712-1.157330487190.5867023112420.05732422828250.611859122715-0.0579199788923-0.04284840214530.396453795149-0.05119061034030.46214925189273.854163443440.14808120919.43547694985
55.658277466871.59958433051-3.045364054662.20492651612-1.127690797785.062269639030.0159621262087-0.120154280426-0.0490205004710.0390097541324-0.0139967442264-0.0112954952084-0.0715890030307-0.1144146982740.006711805383380.3205931196760.0118521345776-0.02884521334190.254778217828-0.01702142550.21844618401970.512612268426.30895761228.66248867661
67.39105542359-2.72575468661-0.7145455646252.02100702992-3.970913215413.86486619432-0.023675836872-0.4336692985440.9740793456-0.227140260857-0.447798067297-0.852640872723-0.4685150757260.3755487582690.2983878425010.668018345856-0.183340284703-0.04438697684470.419266099338-0.00810901846430.55696425591284.70773307440.49325471327.7464760865
73.514095040411.41452956213-0.4315062780875.0283296239-0.229631740767.60593073585-0.04391394386460.0887951010236-0.2589055702010.0884457218176-0.0494337625284-0.2977760391810.05175673850790.4183553911420.06976352531230.3226612429960.06532226635410.0312654885710.327333905568-0.001733452865380.35753888037980.64426579220.66855009673.52586320373
89.36185048123-2.139065743635.647888844443.54047327561-4.121063093636.028912526170.09486223756090.450159121273-0.474000059282-0.09282212281390.492607531986-0.144881288251-0.214339579474-0.288390163562-0.4825772062730.5073868308220.1212417848020.0195421881630.375715596383-0.08863646392130.32354165528576.353059999118.3452967715-3.22930178479
97.348431176570.0578514115478-1.867697995492.05277799088-2.58967211447.17269415480.2543135210910.574506242733-0.520213823079-0.8057323964850.05680832632750.7045670024640.185695589708-1.08035759242-0.1709493653430.424722651991-0.0312162639906-0.05029915557070.556457964915-0.07954610502930.4252760872264.486656296720.2891191451-5.82051809237
101.211727117651.138094017750.824521965234.706850760652.317255650795.049265519770.0601206485655-0.0912667377585-0.132757220.009350449910920.03203526347850.02879150446830.143768101970.00667187342862-0.1057399392950.3036758427-0.02370988612380.02090651314070.3233685440770.02977469454710.28597189540361.083183168124.543809532833.9867020639
117.22942135727-0.3080166411632.581542157433.82710559375-1.318513766453.161504055640.162339040368-0.790111489003-0.1893063226440.180316693288-0.1248778562690.05336845794960.0197495566136-0.1607410794110.01149412347270.402777739111-0.0284148207115-0.008762962293260.349663651948-0.04311739398920.24649302367365.402332305329.715989452937.0019518423
125.889226119751.866185119240.6749707047294.190713340133.68539698317.27441038925-0.00516664695459-0.03511347830170.50536903083-0.0807924870064-0.04594727722160.375661330083-0.416275979759-0.6527736840310.04811006760810.4388667153410.04627454104010.05056420112940.34530292234-0.006395481571160.38976570001758.684715408936.438479452729.4912281187
136.15426440947-1.316357548250.3882450112022.49357120841-0.3865368492522.855502757940.0392355422309-0.5852185800540.746821085080.308254702115-0.113130989115-0.331384336702-0.4883935279140.1697277200410.0703706890670.417269200525-0.08114265464130.006683519795650.369164466024-0.07468327973220.39587687536971.958316873543.43725289139.865010693
145.096406463350.6443071073570.1298113959262.45683037868-1.456788592764.72786604625-0.119229448225-0.8532074584840.5856763349240.5739958668360.05999600267380.165061191759-0.603118769437-0.658472828583-0.02562599020150.5189047815170.0679471787110.05139187869490.624836396771-0.1930588362150.5484533197558.11785433242.377371921947.88607889
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 15 )AA1 - 151 - 15
22chain 'A' and (resid 16 through 51 )AA16 - 5116 - 51
33chain 'A' and (resid 52 through 65 )AA52 - 6552 - 65
44chain 'A' and (resid 66 through 87 )AA66 - 8766 - 87
55chain 'A' and (resid 88 through 148 )AA88 - 14888 - 148
66chain 'A' and (resid 149 through 172 )AA149 - 172149 - 167
77chain 'A' and (resid 173 through 214 )AA173 - 214168 - 209
88chain 'A' and (resid 215 through 229 )AA215 - 229210 - 224
99chain 'A' and (resid 230 through 246 )AA230 - 246225 - 241
1010chain 'B' and (resid 1 through 47 )BD1 - 471 - 47
1111chain 'B' and (resid 48 through 87 )BD48 - 8748 - 87
1212chain 'B' and (resid 88 through 114 )BD88 - 11488 - 114
1313chain 'B' and (resid 115 through 214 )BD115 - 214115 - 214
1414chain 'B' and (resid 215 through 244 )BD - G215 - 244215

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