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- PDB-4usm: WcbL complex with glycerol bound to sugar site -

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Basic information

Entry
Database: PDB / ID: 4usm
TitleWcbL complex with glycerol bound to sugar site
ComponentsPUTATIVE SUGAR KINASE
KeywordsTRANSFERASE / CAPSULAR POLYSACCHARIDE / DRUG DISCOVERY / 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
Biological speciesBURKHOLDERIA PSEUDOMALLEI K96243 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.82 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 10, 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 / 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)76,51112
Polymers76,0432
Non-polymers46810
Water16,502916
1
B: PUTATIVE SUGAR KINASE
hetero molecules

B: PUTATIVE SUGAR KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,51112
Polymers76,0432
Non-polymers46810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4550 Å2
ΔGint-107 kcal/mol
Surface area26330 Å2
MethodPISA
2
A: PUTATIVE SUGAR KINASE
hetero molecules

A: PUTATIVE SUGAR KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,51112
Polymers76,0432
Non-polymers46810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4630 Å2
ΔGint-106.6 kcal/mol
Surface area26310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.050, 115.890, 167.400
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-2142-

HOH

21B-2063-

HOH

31B-2387-

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: (-1, -0.00018, 0.00299), (0.00018, -1, -0.00053), (0.00299, -0.00053, 1)
Vector: -0.12479, -39.46323, -0.00712)

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Components

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


Mass: 38021.383 Da / Num. of mol.: 2
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 916 / 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: 3.23 Å3/Da / Density % sol: 61.6 % / 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: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.82→76.16 Å / Num. obs: 87041 / % possible obs: 99.1 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.4
Reflection shellResolution: 1.82→1.87 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.9 / % possible all: 93.8

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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: 1.82→76.16 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.113 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22872 4345 5 %RANDOM
Rwork0.18994 ---
obs0.19187 82652 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.567 Å2
Baniso -1Baniso -2Baniso -3
1-1.89 Å20 Å20 Å2
2---1.12 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.82→76.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5330 0 20 916 6266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196041
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3391.9598302
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3635855
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92123.758298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.749151102
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9631554
X-RAY DIFFRACTIONr_chiral_restr0.0940.2933
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214712
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_it3.8145.9372940
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.0239.9193717
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.9556.973101
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: 468 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.821→1.868 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 274 -
Rwork0.348 5738 -
obs--93.46 %

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