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

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Basic information

Entry
Database: PDB / ID: 6yus
TitleCapsule O-acetyltransferase of Neisseria meningitidis serogroup A H228A mutant in complex with CoA
ComponentsSacC
KeywordsTRANSFERASE / O-acetyltransferase / a/b hydrolase fold / serine transferase / catalytic triad
Function / homologyUncharacterised protein family (UPF0227) / Alpha/Beta hydrolase fold / COENZYME A / DI(HYDROXYETHYL)ETHER / SacC
Function and homology information
Biological speciesNeisseria meningitidis serogroup A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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 1.2Jan 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)60,5087
Polymers58,6992
Non-polymers1,8095
Water72140
1
A: SacC
B: SacC
hetero molecules

A: SacC
B: SacC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,01614
Polymers117,3984
Non-polymers3,61910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Unit cell
Length a, b, c (Å)136.740, 136.740, 70.760
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

#1: Protein SacC


Mass: 29349.408 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
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.34 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: Native H228A mutant CsaC crystallized in sitting drop setups at concentrations of 18 mg/ml. Fine screens around initial screening conditions resulted in many isomorphous crystals. Mother ...Details: Native H228A mutant 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: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976247 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976247 Å / Relative weight: 1
ReflectionResolution: 2→49.19 Å / Num. obs: 45806 / % possible obs: 100 % / Redundancy: 23.5 % / Biso Wilson estimate: 64.033 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.017 / Rrim(I) all: 0.082 / Net I/σ(I): 20.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.1314.84.5010.574910.1991.19974.66299.9
2.13-2.2924.62.3361.375320.6640.4772.385100
2.29-2.5226.70.9653.775460.9360.1890.983100
2.52-2.8826.80.3621076020.9920.0710.369100
2.88-3.6325.40.10532.776590.9990.0210.107100
3.63-49.1922.80.04473.4797610.0090.107100

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Processing

Software
NameVersionClassification
PHENIX1.18refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YUQ

6yuq


Resolution: 2→49.16 Å / SU ML: 0.3237 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.6456
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.24 2239 5 %
Rwork0.1975 42520 -
obs0.1992 44759 97.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.54 Å2
Refinement stepCycle: LAST / Resolution: 2→49.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3868 0 114 40 4022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00984062
X-RAY DIFFRACTIONf_angle_d1.13995519
X-RAY DIFFRACTIONf_chiral_restr0.0617623
X-RAY DIFFRACTIONf_plane_restr0.006682
X-RAY DIFFRACTIONf_dihedral_angle_d17.66291441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.4361940.43231783X-RAY DIFFRACTION67.01
2.04-2.090.40261370.38752575X-RAY DIFFRACTION96.27
2.09-2.140.3271410.33652701X-RAY DIFFRACTION99.86
2.14-2.20.33521410.30862665X-RAY DIFFRACTION100
2.2-2.270.27371400.27982663X-RAY DIFFRACTION99.96
2.27-2.340.31311420.25162696X-RAY DIFFRACTION100
2.34-2.420.26671400.23922673X-RAY DIFFRACTION99.96
2.42-2.520.25241430.23332711X-RAY DIFFRACTION99.96
2.52-2.630.28531420.22462702X-RAY DIFFRACTION100
2.63-2.770.26271430.22262699X-RAY DIFFRACTION100
2.77-2.950.28051420.22262710X-RAY DIFFRACTION99.96
2.95-3.170.26281440.22662732X-RAY DIFFRACTION100
3.17-3.490.2421440.21362725X-RAY DIFFRACTION100
3.49-40.25161430.18222748X-RAY DIFFRACTION99.97
4-5.040.1791480.16282807X-RAY DIFFRACTION100
5.04-49.160.23571550.17482930X-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)
15.89832389575-0.758808272276-3.270407963225.146458885910.4992696181052.283861909040.3836163334311.39512383418-1.40105950354-0.383520215850.650113867528-0.8445282566911.777914542093.15155740842-1.082170819190.724870086410.33153207717-0.1259594948661.28377251792-0.4386182161721.0398082818111.407792526228.2895874725-22.2267871225
21.90164463947-1.34590477160.1297709583773.129266818370.1177429415774.273569034750.1014675220260.981949823714-0.587912408626-0.5276649035330.33090094115-0.2266826882360.4917291797390.976002468697-0.470930045250.639499588710.00773866245413-0.06886291773261.09517042515-0.3956133598050.6759453172893.6526526165934.7543746041-29.5662602896
33.28702249969-1.824315572870.8908971453051.916954928522.132613079387.6244470131-0.1229118455351.5818204756-0.912010626063-0.6514205402950.541519996906-0.676078067487-0.06169525482241.63072323713-0.3730538302020.671687878456-0.00269815049347-0.04744094238531.29887334092-0.4061042924890.6562194667244.7716414219938.0870991936-30.4224380476
45.487038023081.362118980450.8192966007684.358144024990.1589592330386.11301315565-0.02925728261090.737315773858-0.410853076247-0.2126727043190.514377950858-0.1363653479430.3690000443480.665775642245-0.4500486939270.442712316823-0.00102927216428-0.08355905554880.537448783224-0.1195638384580.409315495092-7.1790964098438.5120205621-26.4575881194
57.30941753282-3.76017365701-0.4645367719454.430383185693.621134401149.86810904563-0.1430575645710.235958813722-1.730281854490.246937504131-0.01693311857470.8952565554281.18612724056-0.62099372417-0.0192110406810.86796423809-0.196260022983-0.2053416136870.5819487296690.03326067102090.872698992855-22.332297366627.6752049996-25.7743245269
63.68744781439-0.2548684825250.3927460848123.58154198208-0.9244445442195.29655316067-0.3848211180641.110109460970.013116210817-0.6538797542720.4505229587420.221792387597-0.3098998966760.0804070621716-0.09917699040050.577242766531-0.202975734094-0.1310283156220.6753141394760.07463687527580.472192129325-14.674170627448.7124260555-33.2822546008
78.08891115052-4.21219240092.537667259179.814700099750.7012744281859.41699037221-0.3210672375351.231926293820.0212165540295-1.178538627040.579044470266-0.543734292871-0.425448776051.66365216151-0.325886002020.787869769604-0.4049850267040.07431992579681.34344144841-0.08364736960360.479393455844-0.0097328103319647.4797233321-41.296721477
81.904546446950.716621816716-3.137585300332.44970987514-0.381496081255.239675606350.2128636809370.0323518733674-0.2262042838950.284651945292-0.136873919682-0.239015201028-0.07983306144210.116058314565-0.09001247487890.44801634760.0625196586592-0.1821888950320.577094059142-0.1584481075910.5440855399934.5011563623142.5927034649-0.122946573822
97.69231539648-4.08459393446-8.694877484824.948178560773.047025718322.042155077990.38496754606-0.5345881408850.4396531330750.6462741700880.00458475934522-0.8149016491230.08953674763011.2647885183-0.4337591022320.6204812418590.0270422841201-0.2203546849710.821811292068-0.03808497884180.72047481620513.253701109737.73613759332.92938323328
104.136183300631.37367295383-1.103817297162.05347507753-0.2336793444132.89010858805-0.05250126120540.274573526171-0.4732083890320.172942442406-0.1549977739410.1194881571910.482028274498-0.2407649029320.2077347059940.6155703381070.0217296111259-0.09848931742160.540278693929-0.1930531869990.609430262922-6.8405278632331.66862055990.265072374466
119.08619621052-6.85652069154-4.849315149298.386203309283.554424084885.586229491840.03650250383541.09252558437-1.46819848438-0.410748489739-0.7355851678570.2522412582610.952154122066-0.7322740902940.8728287325880.9716318454470.00324711450143-0.04156829783640.541773632269-0.1753205935690.861118491337-3.7777804126418.3154045081-2.55495864024
126.007611798580.172984110398-2.52147988186.05797409014-0.9893919361476.91403528926-0.43080554916-0.501298026913-0.8690780432960.7676334114970.0521597366165-0.3111592415131.336231887610.432273763210.3330876842310.8212302854890.123802348316-0.01202023985050.5467664532390.09705088740960.6425941697342.11022730622.088993533412.5097451445
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 11 )AA1 - 111 - 11
22chain 'A' and (resid 12 through 52 )AA12 - 5212 - 52
33chain 'A' and (resid 53 through 70 )AA53 - 7053 - 70
44chain 'A' and (resid 71 through 149 )AA71 - 14971 - 149
55chain 'A' and (resid 150 through 172 )AA150 - 172150 - 172
66chain 'A' and (resid 173 through 229 )AA173 - 229173 - 229
77chain 'A' and (resid 230 through 245 )AA230 - 245230 - 245
88chain 'B' and (resid 1 through 52 )BC1 - 521 - 52
99chain 'B' and (resid 53 through 65 )BC53 - 6553 - 65
1010chain 'B' and (resid 66 through 172 )BC66 - 17266 - 172
1111chain 'B' and (resid 173 through 188 )BC173 - 188173 - 188
1212chain 'B' and (resid 189 through 244 )BC189 - 244189 - 244

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