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- PDB-8a0m: Capsular polysaccharide synthesis multienzyme in complex with cap... -

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Basic information

Entry
Database: PDB / ID: 8a0m
TitleCapsular polysaccharide synthesis multienzyme in complex with capsular polymer fragment
ComponentsBcs3
KeywordsBIOSYNTHETIC PROTEIN / Bacterial capsule synthesis
Function / homology
Function and homology information


CDP-glycerol glycerophosphotransferase activity / teichoic acid biosynthetic process / plasma membrane
Similarity search - Function
Domain of unknown function DUF5776 / Domain of unknown function (DUF5776) / CDP-glycerol glycerophosphotransferase / CDP-glycerol glycerophosphotransferase, C-terminal domain / CDP-glycerol glycerophosphotransferase, N-terminal domain / CDP-Glycerol:Poly(glycerophosphate) glycerophosphotransferase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
beta-D-ribosyl-(1->1)-D-ribitol-5-phosphate / Bcs3
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsCifuente, J.O. / Schulze, J. / Bethe, A. / Di Domenico, V. / Litschko, C. / Budde, I. / Eidenberger, L. / Thiesler, H. / Ramon-Roth, I. / Berger, M. ...Cifuente, J.O. / Schulze, J. / Bethe, A. / Di Domenico, V. / Litschko, C. / Budde, I. / Eidenberger, L. / Thiesler, H. / Ramon-Roth, I. / Berger, M. / Claus, H. / DAngelo, C. / Marina, A. / Gerardy-Schahn, R. / Schubert, M. / Guerin, M.E. / Fiebig, T.
Funding support Germany, Spain, United States, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)412824531 Germany
Ministry of Economy and Competitiveness (MINECO)PID2019-105649RB-I00 Spain
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI149297 United States
CitationJournal: Nat.Chem.Biol. / Year: 2023
Title: A multi-enzyme machine polymerizes the Haemophilus influenzae type b capsule.
Authors: Cifuente, J.O. / Schulze, J. / Bethe, A. / Di Domenico, V. / Litschko, C. / Budde, I. / Eidenberger, L. / Thiesler, H. / Ramon Roth, I. / Berger, M. / Claus, H. / D'Angelo, C. / Marina, A. / ...Authors: Cifuente, J.O. / Schulze, J. / Bethe, A. / Di Domenico, V. / Litschko, C. / Budde, I. / Eidenberger, L. / Thiesler, H. / Ramon Roth, I. / Berger, M. / Claus, H. / D'Angelo, C. / Marina, A. / Gerardy-Schahn, R. / Schubert, M. / Guerin, M.E. / Fiebig, T.
History
DepositionMay 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 5, 2023Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Jul 12, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bcs3
B: Bcs3
C: Bcs3
D: Bcs3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)554,61020
Polymers550,1414
Non-polymers4,46816
Water21612
1
A: Bcs3
B: Bcs3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,30510
Polymers275,0712
Non-polymers2,2348
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Bcs3
D: Bcs3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,30510
Polymers275,0712
Non-polymers2,2348
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.911, 232.806, 129.177
Angle α, β, γ (deg.)90.000, 118.390, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 1 through 2 and (name N...
d_2ens_1(chain "B" and ((resid 1 through 2 and (name N...
d_3ens_1(chain "C" and (resid 1 through 11 or (resid 12...
d_4ens_1(chain "D" and ((resid 1 through 2 and (name N...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASPLYSA2 - 186
d_12ens_1ILEASPA265 - 273
d_13ens_1SERVALA281 - 291
d_14ens_1SERLYSA337 - 352
d_15ens_1SERVALA357 - 737
d_16ens_1PROARGA752 - 758
d_17ens_1GLULYSA769 - 957
d_18ens_1LYSSERA967 - 1111
d_19ens_1XXXXXXB
d_21ens_1ASPVALC2 - 206
d_22ens_1SERVALC208 - 604
d_23ens_1PROARGC619 - 625
d_24ens_1GLULYSC629 - 817
d_25ens_1LYSSERC820 - 964
d_26ens_1XXXXXXD
d_31ens_1ASPLYSE1 - 185
d_32ens_1ILEASPE261 - 269
d_33ens_1SERVALE277 - 287
d_34ens_1SERLYSE338 - 353
d_35ens_1SERVALE358 - 738
d_36ens_1PROARGE753 - 759
d_37ens_1GLULYSE770 - 958
d_38ens_1LYSSERE968 - 1112
d_39ens_1XXXXXXF
d_41ens_1ASPLYSG2 - 186
d_42ens_1ILEASPG205 - 213
d_43ens_1SERVALG218 - 228
d_44ens_1SERLYSG233 - 248
d_45ens_1SERARGG253 - 640
d_46ens_1GLUSERG642 - 975
d_47ens_1XXXXXXH

NCS oper:
IDCodeMatrixVector
1given(-0.613422188974, -0.770499578023, 0.173330950327), (-0.771206379811, 0.537122532443, -0.341672511158), (0.170158566679, -0.343263434417, -0.923697069811)15.0609273615, -1.23202338796, -42.3931761162
2given(-0.474487621871, -0.00567630741756, 0.880243873154), (0.00812420804738, -0.999964857513, -0.00206905363111), (0.88022468378, 0.00616954402099, 0.474517062698)35.4927661462, 45.687279396, -22.0053427922
3given(0.449977392843, 0.0678960156482, -0.890455207739), (0.768027448059, -0.538214289897, 0.347072351506), (-0.455690887509, -0.840068752669, -0.29433026659)-9.15206479456, 47.0360451219, -28.8350422788

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Components

#1: Protein
Bcs3 / Bcs3'


Mass: 137535.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: bcs3', bcs3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2ERG0
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-KOF / beta-D-ribosyl-(1->1)-D-ribitol-5-phosphate / (2R,3S,4S)-5-(((2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)oxy)-2,3,4-trihydroxypentyl hydrogen phosphate


Mass: 364.240 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H21O12P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
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: 3.46 Å3/Da / Density % sol: 64.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.06M Magnesium chloride hexahydrate, 0.06M Calcium chloride dihydrate, 0.1M Imidazole, 0.1M MES monohydrate (acid) pH 6.5, MPD, PEG 1000, PEG 3350 (37.5%(v/v)) protein (9.5mg/ml) and ...Details: 0.06M Magnesium chloride hexahydrate, 0.06M Calcium chloride dihydrate, 0.1M Imidazole, 0.1M MES monohydrate (acid) pH 6.5, MPD, PEG 1000, PEG 3350 (37.5%(v/v)) protein (9.5mg/ml) and purified polymer (produced by the multienzyme in-vitro)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.6→63.94 Å / Num. obs: 76828 / % possible obs: 99.71 % / Redundancy: 7.1 % / Biso Wilson estimate: 100.15 Å2 / CC1/2: 0.988 / Rrim(I) all: 0.1831 / Net I/σ(I): 8.79
Reflection shellResolution: 3.6→3.729 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.38 / Num. unique obs: 7658 / CC1/2: 0.796 / Rrim(I) all: 0.8839 / % possible all: 99.75

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2dialsdata reduction
xia2dialsdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold

Resolution: 3.6→63.94 Å / SU ML: 0.4732 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.6007
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.261 3802 4.96 %
Rwork0.2201 72814 -
obs0.2222 76616 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.26 Å2
Refinement stepCycle: LAST / Resolution: 3.6→63.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31944 0 200 12 32156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002632924
X-RAY DIFFRACTIONf_angle_d0.56744908
X-RAY DIFFRACTIONf_chiral_restr0.04254960
X-RAY DIFFRACTIONf_plane_restr0.0045842
X-RAY DIFFRACTIONf_dihedral_angle_d4.91614678
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.839074679165
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.504124700146
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.899801891907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.650.35381370.28922703X-RAY DIFFRACTION99.82
3.65-3.690.371090.28862727X-RAY DIFFRACTION99.54
3.69-3.740.31791300.27692684X-RAY DIFFRACTION99.93
3.74-3.80.32461250.25062719X-RAY DIFFRACTION99.96
3.8-3.850.27771510.24922663X-RAY DIFFRACTION99.93
3.85-3.910.27961320.2552704X-RAY DIFFRACTION99.47
3.91-3.980.29561340.23192675X-RAY DIFFRACTION99.79
3.98-4.050.28721370.21622702X-RAY DIFFRACTION99.96
4.05-4.120.26371600.21072696X-RAY DIFFRACTION99.93
4.12-4.20.27571750.20842624X-RAY DIFFRACTION99.93
4.2-4.290.28761480.21762719X-RAY DIFFRACTION99.9
4.29-4.380.26231340.20482688X-RAY DIFFRACTION99.89
4.38-4.480.25361170.20192724X-RAY DIFFRACTION99.96
4.48-4.590.23791250.19522725X-RAY DIFFRACTION100
4.59-4.720.2491010.19082728X-RAY DIFFRACTION99.96
4.72-4.860.22741620.19532677X-RAY DIFFRACTION100
4.86-5.010.24451270.18732710X-RAY DIFFRACTION99.93
5.01-5.190.24841370.19142712X-RAY DIFFRACTION99.96
5.19-5.40.2461490.19652702X-RAY DIFFRACTION100
5.4-5.640.25151730.20522668X-RAY DIFFRACTION99.96
5.64-5.940.22331680.22112688X-RAY DIFFRACTION100
5.94-6.310.28021250.23622723X-RAY DIFFRACTION100
6.31-6.80.31141230.22912740X-RAY DIFFRACTION100
6.8-7.480.26421870.22882645X-RAY DIFFRACTION99.96
7.48-8.570.22471590.20042714X-RAY DIFFRACTION100
8.57-10.780.22311230.19742743X-RAY DIFFRACTION99.55
10.78-63.940.25851540.25412611X-RAY DIFFRACTION95.34

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