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- PDB-4bqo: Structural insights into WcbI, a novel polysaccharide biosynthesi... -

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Basic information

Entry
Database: PDB / ID: 4bqo
TitleStructural insights into WcbI, a novel polysaccharide biosynthesis enzyme. Native protein without disulfide bond between COA and Cys14.
ComponentsPUTATIVE CAPSULAR POLYSACCHARIDE BIOSYNTHESIS PROTEIN
KeywordsTRANSFERASE / ACETYLTRANSFERASE / MELIOIDOSIS
Function / homology
Function and homology information


Arc Repressor Mutant, subunit A - #2490 / Rossmann fold - #12080 / Polysaccharide biosynthesis enzyme WcbI / Polysaccharide biosynthesis enzyme WcbI / Arc Repressor Mutant, subunit A / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / COENZYME A / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Capsular polysaccharide biosynthesis protein
Similarity search - Component
Biological speciesBURKHOLDERIA PSEUDOMALLEI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.56 Å
AuthorsVivoli, M. / Ayres, E. / Isupov, M.N. / Harmer, N.J.
CitationJournal: Iucrj / Year: 2014
Title: Structural Insights Into Wcbi, a Novel Polysaccharide-Biosynthesis Enzyme.
Authors: Vivoli, M. / Ayres, E. / Beaumont, E. / Isupov, M.N. / Harmer, N.J.
History
DepositionMay 31, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Aug 13, 2014Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: PUTATIVE CAPSULAR POLYSACCHARIDE BIOSYNTHESIS PROTEIN
B: PUTATIVE CAPSULAR POLYSACCHARIDE BIOSYNTHESIS PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,13245
Polymers72,1982
Non-polymers4,93443
Water12,556697
1
A: PUTATIVE CAPSULAR POLYSACCHARIDE BIOSYNTHESIS PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,80125
Polymers36,0991
Non-polymers2,70224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PUTATIVE CAPSULAR POLYSACCHARIDE BIOSYNTHESIS PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,33120
Polymers36,0991
Non-polymers2,23219
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.200, 67.900, 71.900
Angle α, β, γ (deg.)62.90, 76.20, 69.80
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99496, 0.02571, 0.09694), (0.01803, -0.99669, 0.07933), (0.09866, -0.07718, -0.99212)
Vector: -29.85524, 167.77513, 88.77119)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PUTATIVE CAPSULAR POLYSACCHARIDE BIOSYNTHESIS PROTEIN / WCBI


Mass: 36098.941 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA PSEUDOMALLEI (bacteria) / Strain: K96243 / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q63R74

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Non-polymers , 5 types, 740 molecules

#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical...
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: Br
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 697 / 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: 2.63 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 7
Details: 10% (W/V) PEG 8000, 75 MM LICL, 75 MM MGCL2, 0.05 M HEPES PH 7.0-8.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 23, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.56→63.7 Å / Num. obs: 92966 / % possible obs: 92 % / Redundancy: 3.9 % / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13
Reflection shellResolution: 1.56→1.6 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.2 / % possible all: 72.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
xia2data reduction
SCALAdata scaling
SHELXphasing
ARPphasing
WARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.56→44 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.634 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2129 4877 5 %RANDOM
Rwork0.17713 ---
obs0.17894 92900 91.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.464 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å20.12 Å2-0.35 Å2
2---1.26 Å20.43 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.56→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5027 0 158 697 5882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195835
X-RAY DIFFRACTIONr_bond_other_d1.5271.9898006
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5675760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.40422.914302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.785151026
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4291562
X-RAY DIFFRACTIONr_chiral_restr0.1020.2828
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214592
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_it3.4296.5022660
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.67510.9533364
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.2617.5613175
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it827.92926052
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.557→1.598 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 294 -
Rwork0.291 5369 -
obs--72.52 %

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