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- PDB-4usk: Unravelling the B. pseudomallei heptokinase WcbL: from Structure ... -

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Basic information

Entry
Database: PDB / ID: 4usk
TitleUnravelling the B. pseudomallei heptokinase WcbL: from Structure to Drug Discovery.
ComponentsPUTATIVE SUGAR KINASE
KeywordsTRANSFERASE / CAPSULAR POLYSACCHARIDE / HEPTOPYRANOSE
Function / homology
Function and homology information


fucokinase activity / GDP-L-fucose salvage / ATP binding
Similarity search - Function
D,D-heptose 7-phosphate kinase / : / Galactokinase/homoserine kinase / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 ...D,D-heptose 7-phosphate kinase / : / Galactokinase/homoserine kinase / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
S-1,2-PROPANEDIOL / Sugar kinase
Similarity search - Component
Biological speciesBURKHOLDERIA PSEUDOMALLEI K96243 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å
AuthorsVivoli, M. / Isupov, M.N. / Nicholas, R. / Hill, A. / Scott, A. / Kosma, P. / Prior, J. / Harmer, N.J.
CitationJournal: Chem.Biol. / Year: 2015
Title: Unraveling the B.Pseudomallei Heptokinase Wcbl: From Structure to Drug Discovery.
Authors: Vivoli, M. / Isupov, M.N. / Nicholas, R. / Hill, A. / Scott, A.E. / Kosma, P. / Prior, J.L. / Harmer, N.J.
History
DepositionJul 9, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_special_symmetry / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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: PUTATIVE SUGAR KINASE
B: PUTATIVE SUGAR KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,28115
Polymers75,6952
Non-polymers58713
Water15,223845
1
B: PUTATIVE SUGAR KINASE
hetero molecules

B: PUTATIVE SUGAR KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,35816
Polymers75,6952
Non-polymers66314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5230 Å2
ΔGint-117 kcal/mol
Surface area26270 Å2
MethodPISA
2
A: PUTATIVE SUGAR KINASE
hetero molecules

A: PUTATIVE SUGAR KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,20514
Polymers75,6952
Non-polymers51112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4750 Å2
ΔGint-122.4 kcal/mol
Surface area25880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.580, 116.050, 168.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-40-

ASP

21A-2121-

HOH

31A-2122-

HOH

41A-2471-

HOH

51B-2046-

HOH

61B-2346-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 2 - 346 / Label seq-ID: 2 - 346

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-0.99998, 0.00021, 0.00587), (-0.0002, -1, 0.00107), (0.00587, 0.00107, 0.99998)
Vector: -0.24929, -40.12203, 0.01631)

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Components

#1: Protein PUTATIVE SUGAR KINASE / WCBL / D-GLYCERO-BETA-D-MANNO-HEPTOSE-7-PHOSPHATE KINASE


Mass: 37847.277 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA PSEUDOMALLEI K96243 (bacteria)
Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA / References: UniProt: H7C745, EC: 2.7.1.167
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 845 / 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: 3.26 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growpH: 7 / Details: 0.5 M NACL, 10 MM HEPES PH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Aug 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.76→48.62 Å / Num. obs: 96595 / % possible obs: 98.4 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.6
Reflection shellResolution: 1.76→1.81 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 1.9 / % possible all: 96.6

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Processing

Software
NameVersionClassification
xia2data reduction
XDSdata reduction
Aimlessdata scaling
SHELXphasing
ARP/wARPphasing
REFMAC5.8.0073refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.76→48.62 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.978 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23695 4827 5 %RANDOM
Rwork0.19948 ---
obs0.20137 91724 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.862 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20 Å2
2---1.07 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.76→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5306 0 23 845 6174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196079
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.461.9588374
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5185873
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4623.356289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.761151104
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5031557
X-RAY DIFFRACTIONr_chiral_restr0.10.2953
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214735
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_it4.1366.1842972
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.21710.3353767
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.1836.9653103
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 459 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 332 -
Rwork0.321 6582 -
obs--96.58 %

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