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- PDB-2q6v: Crystal Structure of GumK in complex with UDP -

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Basic information

Entry
Database: PDB / ID: 2q6v
TitleCrystal Structure of GumK in complex with UDP
ComponentsGlucuronosyltransferase GumK
KeywordsTRANSFERASE / Glucuronosyltransferase / glycosyltransferase / xanthan / Xanthomonas campestris / UDP / UDPGlcA
Function / homology
Function and homology information


D-Man-alpha-(1->3)-D-Glc-beta-(1->4)-D-Glc-alpha-1-diphosphoundecaprenol 2-beta-glucuronosyltransferase / glucuronosyltransferase activity / polysaccharide biosynthetic process / plasma membrane
Similarity search - Function
Rossmann fold - #11010 / : / Glucuronosyltransferase GumK, N-terminal domain / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / UDP-glucuronate:glycolipid 2-beta-glucuronosyltransferase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ARP/wARP / Resolution: 2.28 Å
AuthorsBarreras, M.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structure and mechanism of GumK, a membrane-associated glucuronosyltransferase.
Authors: Barreras, M. / Salinas, S.R. / Abdian, P.L. / Kampel, M.A. / Ielpi, L.
History
DepositionJun 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: Glucuronosyltransferase GumK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7402
Polymers45,3351
Non-polymers4041
Water7,584421
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.210, 121.210, 170.724
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1083-

HOH

21A-1268-

HOH

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Components

#1: Protein Glucuronosyltransferase GumK


Mass: 45335.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Gene: gumK / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8GCH2, glucuronosyltransferase
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H2O

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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: 3.99 Å3/Da / Density % sol: 69.19 %
Crystal growTemperature: 293 K / Method: hanging drop, soaking of crystals in udpglca 100 mm / pH: 8.2
Details: 0.1 M Tris-HCl, 35% (w/v) PEG 3350, 0.2 M Li2SO4, 0.1 M LiCl, pH 8.2, hanging drop and soaking of crystals in UDPGlcA 100 mM, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.427 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 13, 2006 / Details: beam focused by a cilindrically curved mirror
RadiationMonochromator: Silicium curved crystal, with asymmetric 7.25 angle cut
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.427 Å / Relative weight: 1
ReflectionResolution: 2.28→104.971 Å / Num. obs: 33916 / % possible obs: 98.5 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 4.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym value% possible all
2.28-2.49.10.3032.20.30393.8
2.4-2.5510.40.25120.251100
2.55-2.7210.30.2131.40.21399.9
2.72-2.9410.30.1354.90.13599.8
2.94-3.2210.30.113.70.1199.6
3.22-3.610.30.0975.60.09799.5
3.6-4.1610.30.0855.90.08599.2
4.16-5.0910.50.0568.90.05698.7
5.09-7.210.30.05412.20.05498.1
7.2-27.069.60.04214.20.04295

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
ARP/wARPmodel building
RefinementMethod to determine structure: ARP/wARP
Starting model: PDB entry 2HY7 Apo protein GumK

2hy7


Resolution: 2.28→104.83 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.644 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21641 1714 5.1 %RANDOM
Rwork0.17541 ---
obs0.17746 32197 98.51 %-
all-32197 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.077 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.28→104.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2935 0 25 421 3381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223045
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.9544154
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5495369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.79521.958143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38215458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6781530
X-RAY DIFFRACTIONr_chiral_restr0.1050.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022372
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.21910
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.22134
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2485
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.241
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.081.51895
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.63923000
X-RAY DIFFRACTIONr_scbond_it2.81231313
X-RAY DIFFRACTIONr_scangle_it4.3714.51154
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 108 -
Rwork0.199 2183 -
obs--92.27 %

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