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- PDB-3cv3: Crystal Structure of GumK mutant D157A in complex with UDP -

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Basic information

Entry
Database: PDB / ID: 3cv3
TitleCrystal Structure of GumK mutant D157A 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 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
DepositionApr 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Source and taxonomy
Category: database_2 / entity_src_gen ...database_2 / entity_src_gen / 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 / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: 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

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Assembly

Deposited unit
A: Glucuronosyltransferase GumK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6962
Polymers45,2911
Non-polymers4041
Water7,602422
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.958, 120.958, 171.031
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1083-

HOH

21A-1391-

HOH

31A-1447-

HOH

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Components

#1: Protein Glucuronosyltransferase GumK


Mass: 45291.426 Da / Num. of mol.: 1 / Mutation: D157A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Gene: gumK / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / 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.: 422 / 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: 69.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / 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 10 mM, temperature 293K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.433 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 1, 2008 / 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: 1.433 Å / Relative weight: 1
ReflectionResolution: 2.25→17.46 Å / Num. obs: 35644 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 14.9 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.149 / Rsym value: 0.149 / Net I/σ(I): 16.8
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 10.1 / Num. unique all: 5131 / Rsym value: 0.297 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.5data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2HY7

2hy7


Resolution: 2.25→17.46 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.894 / SU B: 3.927 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1785 5 %RANDOM
Rwork0.173 ---
obs0.175 35598 99.98 %-
all-35607 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.864 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.25→17.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2925 0 25 422 3372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223034
X-RAY DIFFRACTIONr_angle_refined_deg1.9441.9524138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8765368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.98721.901142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72115457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7611530
X-RAY DIFFRACTIONr_chiral_restr0.1340.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022360
X-RAY DIFFRACTIONr_nbd_refined0.2470.21978
X-RAY DIFFRACTIONr_nbtor_refined0.3310.22151
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2461
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.232
X-RAY DIFFRACTIONr_mcbond_it0.9051.51871
X-RAY DIFFRACTIONr_mcangle_it1.5322988
X-RAY DIFFRACTIONr_scbond_it2.53531304
X-RAY DIFFRACTIONr_scangle_it4.0224.51150
LS refinement shellResolution: 2.25→2.307 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 126 -
Rwork0.188 2420 -
all-2546 -
obs--100 %

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