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

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Basic information

Entry
Database: PDB / ID: 4bqn
TitleStructural insights into WcbI, a novel polysaccharide biosynthesis enzyme. Native protein.
ComponentsCAPSULAR 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
COENZYME A / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Capsular polysaccharide biosynthesis protein
Similarity search - Component
Biological speciesBURKHOLDERIA PSEUDOMALLEI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.38 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 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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_label_seq_id / _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: CAPSULAR POLYSACCHARIDE BIOSYNTHESIS PROTEIN
B: CAPSULAR POLYSACCHARIDE BIOSYNTHESIS PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,48514
Polymers72,1982
Non-polymers2,28712
Water18,7541041
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A: CAPSULAR POLYSACCHARIDE BIOSYNTHESIS PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2218
Polymers36,0991
Non-polymers1,1227
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CAPSULAR POLYSACCHARIDE BIOSYNTHESIS PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2646
Polymers36,0991
Non-polymers1,1655
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.920, 68.000, 71.490
Angle α, β, γ (deg.)63.04, 76.45, 69.95
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.995, 0.01996, 0.09785), (0.02788, -0.99638, -0.08031), (0.0959, 0.08264, -0.99196)
Vector: -28.46154, 179.68954, 60.00501)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 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, 1053 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.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1041 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: I24 / Wavelength: 0.9778
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Oct 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.38→24.15 Å / Num. obs: 397472 / % possible obs: 92.3 % / Redundancy: 2.8 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.02 / Net I/σ(I): 55.9
Reflection shellResolution: 1.38→1.42 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 5.7 / % possible all: 59.4

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Processing

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

Resolution: 1.38→24.63 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.972 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.15502 7032 5 %RANDOM
Rwork0.1165 ---
obs0.11846 132676 92.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.683 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å2-0.03 Å20.09 Å2
2---0.69 Å20.15 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.38→24.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5046 0 139 1041 6226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.026237
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.9988631
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.385854
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.14323.776331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.479151144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0011558
X-RAY DIFFRACTIONr_chiral_restr0.0880.2892
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214978
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_it2.4184.3912795
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.0087.4463565
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.4285.3893442
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.40636237
X-RAY DIFFRACTIONr_sphericity_free40.556547
X-RAY DIFFRACTIONr_sphericity_bonded19.07356973
LS refinement shellResolution: 1.38→1.416 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 326 -
Rwork0.155 6407 -
obs--60.53 %

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