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- PDB-6u4b: WbbM bifunctional glycosytransferase apo structure -

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Basic information

Entry
Database: PDB / ID: 6u4b
TitleWbbM bifunctional glycosytransferase apo structure
ComponentsWbbM protein
KeywordsTRANSFERASE / Glycsoyltransferase / bifunctional / trimeric / WbbM / DUF4422
Function / homologyDomain of unknown function DUF4422 / Domain of unknown function (DUF4422) / : / Glycosyl transferase, family 8 / Glycosyl transferase family 8 / glycosyltransferase activity / Nucleotide-diphospho-sugar transferases / metal ion binding / WbbM protein
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsKimber, M.S. / Mallette, E. / Kamski-Hennekam, E.R. / Gitalis, R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)04045-2015 Canada
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: A bifunctional O-antigen polymerase structure reveals a new glycosyltransferase family.
Authors: Clarke, B.R. / Ovchinnikova, O.G. / Sweeney, R.P. / Kamski-Hennekam, E.R. / Gitalis, R. / Mallette, E. / Kelly, S.D. / Lowary, T.L. / Kimber, M.S. / Whitfield, C.
History
DepositionAug 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.2Mar 13, 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: WbbM protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7463
Polymers69,6981
Non-polymers492
Water3,387188
1
A: WbbM protein
hetero molecules

A: WbbM protein
hetero molecules

A: WbbM protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,2399
Polymers209,0933
Non-polymers1466
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_745-y+2,x-y-1,z1
crystal symmetry operation3_875-x+y+3,-x+2,z1
Buried area6160 Å2
ΔGint-76 kcal/mol
Surface area68470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.030, 124.030, 73.050
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Components on special symmetry positions
IDModelComponents
11A-601-

MG

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Components

#1: Protein WbbM protein


Mass: 69697.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: wbbM / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q48484
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.46 Å3/Da / Density % sol: 50.01 % / Description: hexagonal prisms
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 50 mM MgCl, 0.1 M HEPES and 30% v/v PEG MME 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jan 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.1→47.288 Å / Num. obs: 37124 / % possible obs: 99 % / Redundancy: 5.7 % / Biso Wilson estimate: 39.05 Å2 / Rsym value: 0.068 / Net I/σ(I): 14.7
Reflection shellResolution: 2.1→2.15 Å / Mean I/σ(I) obs: 2.05 / Num. unique obs: 2755 / CC1/2: 0.83 / Rsym value: 0.08

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→47.28 Å / SU ML: 0.2537 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.3833
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2269 1855 5 %
Rwork0.1883 35247 -
obs0.1902 37102 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.39 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4655 0 2 188 4845
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00244774
X-RAY DIFFRACTIONf_angle_d0.52346470
X-RAY DIFFRACTIONf_chiral_restr0.0429692
X-RAY DIFFRACTIONf_plane_restr0.0034836
X-RAY DIFFRACTIONf_dihedral_angle_d17.82922821
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.37881420.31692693X-RAY DIFFRACTION99.47
2.16-2.220.34391440.29012734X-RAY DIFFRACTION99.65
2.22-2.290.3291420.26842711X-RAY DIFFRACTION99.58
2.29-2.370.26941400.24482685X-RAY DIFFRACTION99.54
2.37-2.470.30551440.23082717X-RAY DIFFRACTION99.51
2.47-2.580.33331430.22632730X-RAY DIFFRACTION99.48
2.58-2.720.25691420.22382684X-RAY DIFFRACTION99.12
2.72-2.890.26061440.21132731X-RAY DIFFRACTION99.45
2.89-3.110.27021420.21052706X-RAY DIFFRACTION98.96
3.11-3.420.23021420.19752707X-RAY DIFFRACTION98.82
3.42-3.920.21411430.16822706X-RAY DIFFRACTION98.55
3.92-4.940.17761430.14162713X-RAY DIFFRACTION98.14
4.94-47.280.16331440.15422730X-RAY DIFFRACTION97
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)
14.03300261929-0.9276978108510.1651296502154.420409993240.5003522621381.886699641810.1713130168460.130865369889-0.8179793255490.0281265412591-0.08255311544170.2993286527160.253735171679-0.202988808651-0.09302903078360.285672228416-0.02601425143080.06043695340920.339669391508-0.04457273191470.640525741194142.1999894818.6781753413-14.8720593597
23.986073636930.322943182553-0.07634172403142.872705614340.7546055663421.984865384440.1354963335430.0258090967403-0.108193424340.0337476973348-0.1646587359360.6656757397920.0368930678734-0.3491711492750.05538306572420.271827275915-0.00555677265270.04691171036980.3938836334240.03944984784690.601009172564130.28837938432.1083254723-10.3124864869
35.64956936921-0.9748505860210.4882505183520.9972187943060.158554867320.610226553945-0.06415415036910.0953335294628-0.2474593846690.0423924944175-0.02718524013950.2267610921850.00277289936904-0.1395407721270.09203451404870.291345526157-0.0189306806270.0280138274420.282307854341-0.004074432859090.627032731207157.43924109517.0496486589-12.3119998477
43.11493767022-0.117557459523-0.3971994540722.72387531454-0.3321548950841.0034364613-0.00237423972311-0.0934750270269-0.07425501945650.131971911267-0.1251440142380.2729505491360.137547560546-0.1155316197890.1026526729780.297912096674-0.01799140119310.05887881176270.31255403463-0.01381584907930.476728708523172.0030043489.95932602126-9.76677183715
55.30048897065-0.8666120358460.7886431020722.13282238587-1.001077891232.13554927991-0.0197283723438-0.246269587649-0.6370359757380.108011266945-0.1313448522830.03402260154370.3579550432340.128693584160.1444763273860.3518336963070.02182765920260.08152302251460.276057745947-0.01700082272250.570508923933177.214633384-2.36502995278-7.25076673189
63.68550567396-3.597888959470.3758793296966.734922516940.8426162814790.0097705159131-0.326238910101-0.3939624160280.3754649788060.7377733635350.255637763368-0.05889191265950.05957205209930.05745003203560.02548370221330.418134493277-0.009532117095210.03096086108940.4304340728690.05480325860770.650167315815187.60680379218.3673788527-2.32083718077
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 119 )
2X-RAY DIFFRACTION2chain 'A' and (resid 120 through 252 )
3X-RAY DIFFRACTION3chain 'A' and (resid 253 through 305 )
4X-RAY DIFFRACTION4chain 'A' and (resid 306 through 434 )
5X-RAY DIFFRACTION5chain 'A' and (resid 435 through 522 )
6X-RAY DIFFRACTION6chain 'A' and (resid 523 through 578 )

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