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- PDB-3q3h: Crystal structure of the Actinobacillus pleuropneumoniae HMW1C gl... -

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Basic information

Entry
Database: PDB / ID: 3q3h
TitleCrystal structure of the Actinobacillus pleuropneumoniae HMW1C glycosyltransferase in complex with UDP-GLC
ComponentsHMW1C-like glycosyltransferase
KeywordsTRANSFERASE / HMW1C / HMW1 / N-glycosylation
Function / homologyRossmann fold - #11380 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / URIDINE-5'-DIPHOSPHATE / :
Function and homology information
Biological speciesActinobacillus pleuropneumoniae serovar 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.25 Å
AuthorsKawai, F. / Yeo, H.J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural Insights into the Glycosyltransferase Activity of the Actinobacillus pleuropneumoniae HMW1C-like Protein.
Authors: Kawai, F. / Grass, S. / Kim, Y. / Choi, K.J. / St Geme, J.W. / Yeo, H.J.
History
DepositionDec 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references
Revision 1.2Nov 16, 2011Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HMW1C-like glycosyltransferase
B: HMW1C-like glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,7346
Polymers143,7412
Non-polymers9934
Water5,044280
1
A: HMW1C-like glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2752
Polymers71,8711
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HMW1C-like glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4594
Polymers71,8711
Non-polymers5883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.245, 94.896, 176.791
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HMW1C-like glycosyltransferase / adhesin processing HMWC-like protein


Mass: 71870.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinobacillus pleuropneumoniae serovar 1 (bacteria)
Strain: 4074 / Gene: APL_1635, appser1_17560 / Plasmid: PET45B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E0EAD4
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsS428P POSSIBLE NATURAL VARIANT

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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: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES, 0.1-0.16 M ammonium sulfate, 20-30% w/v PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97943
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2009
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 61133 / % possible obs: 92.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.084
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.271 / % possible all: 74.2

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Processing

Software
NameVersionClassification
HKL-3000data collection
SHELXmodel building
REFMAC5.5.0109refinement
HKL-3000data reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: SIR / Resolution: 2.25→41.81 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / SU B: 7.143 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.244 3065 5.1 %RANDOM
Rwork0.186 ---
obs0.189 60467 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å2-0 Å2
2--0.6 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.25→41.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9736 0 62 280 10078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02210035
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8121.95513628
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.72351211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.85124.049489
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.895151674
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4551558
X-RAY DIFFRACTIONr_chiral_restr0.1220.21512
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217650
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9491.56071
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.81829836
X-RAY DIFFRACTIONr_scbond_it2.89733964
X-RAY DIFFRACTIONr_scangle_it4.7264.53792
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 181 -
Rwork0.263 3332 -
obs--100 %

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