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- PDB-5bvc: Crystal structure of Lipomyces starkeyi levoglucosan kinase bound... -

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Basic information

Entry
Database: PDB / ID: 5bvc
TitleCrystal structure of Lipomyces starkeyi levoglucosan kinase bound to ADP, magnesium and levoglucosan in an alternate orientation.
ComponentsLevoglucosan kinase
KeywordsTRANSFERASE / SUGAR KINASE / ATP-BINDING / CARBOHYDRATE METABOLISM / LEVOGLUCOSAN
Function / homology
Function and homology information


levoglucosan kinase / amino sugar metabolic process / phosphotransferase activity, alcohol group as acceptor / peptidoglycan turnover / kinase activity / ATP binding / metal ion binding
Similarity search - Function
Anhydro-N-acetylmuramic acid kinase / Anhydro-N-acetylmuramic acid kinase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Levoglucosan / ADENOSINE-5'-DIPHOSPHATE / Levoglucosan kinase
Similarity search - Component
Biological speciesLipomyces starkeyi (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBacik, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Producing Glucose 6-Phosphate from Cellulosic Biomass: STRUCTURAL INSIGHTS INTO LEVOGLUCOSAN BIOCONVERSION.
Authors: Bacik, J.P. / Klesmith, J.R. / Whitehead, T.A. / Jarboe, L.R. / Unkefer, C.J. / Mark, B.L. / Michalczyk, R.
History
DepositionJun 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Nov 11, 2015Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Levoglucosan kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0104
Polymers49,3961
Non-polymers6143
Water5,260292
1
A: Levoglucosan kinase
hetero molecules

A: Levoglucosan kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0198
Polymers98,7922
Non-polymers1,2276
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6580 Å2
ΔGint-59 kcal/mol
Surface area29070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.250, 70.250, 264.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Levoglucosan kinase


Mass: 49395.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lipomyces starkeyi (fungus) / Production host: Escherichia coli (E. coli)
References: UniProt: B3VI55, Transferases; Transferring phosphorus-containing groups
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-4PW / Levoglucosan / (1R,2S,3S,4R,5R)-6,8-dioxabicyclo[3.2.1]octane-2,3,4-triol


Mass: 162.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O5
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 3.3 Å3/Da / Density % sol: 62.72 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: Equal amounts of LGK (25 mg/ml) in crystallization buffer (100 mM NaCl, 0.5 mM TCEP, 20 mM Tris pH 7.5, 2 mM ADP, 4 mM MgCl, 1 mM aluminum nitrate and 10 mM sodium fluoride) and ...Details: Equal amounts of LGK (25 mg/ml) in crystallization buffer (100 mM NaCl, 0.5 mM TCEP, 20 mM Tris pH 7.5, 2 mM ADP, 4 mM MgCl, 1 mM aluminum nitrate and 10 mM sodium fluoride) and crystallization buffer (1.3 M sodium malonate, 0.093 M Bis-Tris Propane pH 7.0) were mixed and and a resultant crystal was soaked with 200 mM levoglucosan.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 2→43.27 Å / Num. obs: 44939 / % possible obs: 98.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.2
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YH5

4yh5


Resolution: 2→43.27 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.232 2271 5.07 %
Rwork0.2036 --
obs0.2051 44796 97.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→43.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3279 0 39 292 3610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083390
X-RAY DIFFRACTIONf_angle_d1.1174618
X-RAY DIFFRACTIONf_dihedral_angle_d14.2811236
X-RAY DIFFRACTIONf_chiral_restr0.074521
X-RAY DIFFRACTIONf_plane_restr0.005619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04350.32131290.3052662X-RAY DIFFRACTION100
2.0435-2.0910.32151420.31352649X-RAY DIFFRACTION99
2.091-2.14330.29681780.2722614X-RAY DIFFRACTION99
2.1433-2.20130.33221220.24562679X-RAY DIFFRACTION99
2.2013-2.26610.28841420.28442635X-RAY DIFFRACTION98
2.2661-2.33920.26081450.24332603X-RAY DIFFRACTION98
2.3392-2.42280.28251510.22452648X-RAY DIFFRACTION98
2.4228-2.51980.28491360.22932619X-RAY DIFFRACTION98
2.5198-2.63450.24421350.2032645X-RAY DIFFRACTION98
2.6345-2.77330.23361430.20672638X-RAY DIFFRACTION98
2.7733-2.9470.22351280.19852664X-RAY DIFFRACTION97
2.947-3.17450.22531370.19042661X-RAY DIFFRACTION97
3.1745-3.49390.2331610.18632642X-RAY DIFFRACTION97
3.4939-3.99910.19251390.16432646X-RAY DIFFRACTION96
3.9991-5.03730.18661340.16572662X-RAY DIFFRACTION94
5.0373-43.27580.19931490.20032858X-RAY DIFFRACTION95

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