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- PDB-4utg: Burkholderia pseudomallei heptokinase WcbL,AMPPNP (ATP analogue) ... -

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Basic information

Entry
Database: PDB / ID: 4utg
TitleBurkholderia pseudomallei heptokinase WcbL,AMPPNP (ATP analogue) complex.
ComponentsSUGAR KINASE
KeywordsTRANSFERASE / CAPSULAR POLYSACCHARIDE / DRUG DISCOVERY / HEPTOPYRANOSE
Function / homology
Function and homology information


kinase activity / phosphorylation / ATP binding / metal ion 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 / Ribosomal Protein S5; domain 2 ...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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Sugar kinase
Similarity search - Component
Biological speciesBURKHOLDERIA PSEUDOMALLEI K96243 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.93 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 21, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SUGAR KINASE
B: SUGAR KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,02212
Polymers75,6952
Non-polymers1,32710
Water10,917606
1
A: SUGAR KINASE
hetero molecules

A: SUGAR KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,02212
Polymers75,6952
Non-polymers1,32710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5770 Å2
ΔGint-81 kcal/mol
Surface area25620 Å2
MethodPISA
2
B: SUGAR KINASE
hetero molecules

B: SUGAR KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,02212
Polymers75,6952
Non-polymers1,32710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5720 Å2
ΔGint-77.8 kcal/mol
Surface area26040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.440, 115.020, 166.780
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-2134-

HOH

21A-2234-

HOH

31B-2259-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, -0.00046, -0.00025), (0.00046, -1, -0.00312), (-0.00025, -0.00312, 1)
Vector: 0.01678, -39.74981, -0.05549)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 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 (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: H7C745, EC: 2.7.1.167

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Non-polymers , 5 types, 616 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 606 / 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: 3.21 Å3/Da / Density % sol: 61.4 % / Description: NONE
Crystal growpH: 7 / Details: 0.5 M NACL, 10 MM HEPES PH 7, 25 MM AMPPNP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: May 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.93→76.08 Å / Num. obs: 72694 / % possible obs: 99.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.8
Reflection shellResolution: 1.93→1.98 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.1 / % possible all: 96.7

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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: 1.93→76.08 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.098 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2416 3690 5.1 %RANDOM
Rwork0.19399 ---
obs0.19637 68961 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.427 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2---1.62 Å20 Å2
3---1.54 Å2
Refinement stepCycle: LAST / Resolution: 1.93→76.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5306 0 76 606 5988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196197
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.9718565
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0535888
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.02223.356292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.688151119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5221558
X-RAY DIFFRACTIONr_chiral_restr0.0860.2974
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024806
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_it4.3117.6732990
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.30612.8533794
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.378.7733206
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
LS refinement shellResolution: 1.934→1.984 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 264 -
Rwork0.315 4884 -
obs--96.66 %

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