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- PDB-5tkr: Crystal structure of a Lipomyces starkeyi levoglucosan kinase G35... -

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Basic information

Entry
Database: PDB / ID: 5tkr
TitleCrystal structure of a Lipomyces starkeyi levoglucosan kinase G359R mutant
ComponentsLevoglucosan kinase
KeywordsTRANSFERASE / SUGAR KINASE / ATP-BINDING / CARBOHYDRATE METABOLISM / LEVOGLUCOSAN / MUTANT
Function / homology
Function and homology information


levoglucosan kinase / amino sugar metabolic process / phosphotransferase activity, alcohol group as acceptor / peptidoglycan turnover / kinase activity / phosphorylation / ATP binding / metal ion binding
Similarity search - Function
Anhydro-N-acetylmuramic acid kinase / Anhydro-N-acetylmuramic acid kinase / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / Levoglucosan kinase
Similarity search - Component
Biological speciesLipomyces starkeyi (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBacik, J.P. / Klesmith, J.R. / Michalczyk, R. / Whitehead, T.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Trade-offs between enzyme fitness and solubility illuminated by deep mutational scanning.
Authors: Klesmith, J.R. / Bacik, J.P. / Wrenbeck, E.E. / Michalczyk, R. / Whitehead, T.A.
History
DepositionOct 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Mar 15, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Levoglucosan kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2447
Polymers49,5941
Non-polymers6506
Water8,287460
1
A: Levoglucosan kinase
hetero molecules

A: Levoglucosan kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,48814
Polymers99,1882
Non-polymers1,30012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area8360 Å2
ΔGint-127 kcal/mol
Surface area29050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.060, 70.060, 261.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Levoglucosan kinase


Mass: 49594.156 Da / Num. of mol.: 1 / Mutation: G359R
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

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Non-polymers , 5 types, 466 molecules

#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / 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: 3.24 Å3/Da / Density % sol: 62.02 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: Crystals were grown using the hanging drop vapor-diffusion method by mixing equal volumes of reservoir buffer (22% PEG3350, 0.2 M K2SO4, 100 mM Tris pH 6.8) and LGK (23 mg/ml) in ...Details: Crystals were grown using the hanging drop vapor-diffusion method by mixing equal volumes of reservoir buffer (22% PEG3350, 0.2 M K2SO4, 100 mM Tris pH 6.8) and LGK (23 mg/ml) in crystallization buffer (50 mM NaCl, 2 mM ADP, 4 mM MgCl2 , 0.5 mM TCEP, 20 mM Tris pH 7.5).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97947 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.8→46.33 Å / Num. obs: 61638 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 9.4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.045 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BSB

5bsb


Resolution: 1.8→43.081 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.82
RfactorNum. reflection% reflection
Rfree0.2079 3097 5.03 %
Rwork0.175 --
obs0.1767 61556 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→43.081 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3329 0 36 467 3832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083450
X-RAY DIFFRACTIONf_angle_d0.8284676
X-RAY DIFFRACTIONf_dihedral_angle_d13.7991273
X-RAY DIFFRACTIONf_chiral_restr0.053520
X-RAY DIFFRACTIONf_plane_restr0.005628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82810.28291360.27092579X-RAY DIFFRACTION100
1.8281-1.85810.29881460.26822593X-RAY DIFFRACTION100
1.8581-1.89010.31881460.25232602X-RAY DIFFRACTION100
1.8901-1.92450.2621250.25042618X-RAY DIFFRACTION100
1.9245-1.96150.27961330.22392622X-RAY DIFFRACTION100
1.9615-2.00160.24591380.2072640X-RAY DIFFRACTION100
2.0016-2.04510.22321260.2052602X-RAY DIFFRACTION100
2.0451-2.09270.22071420.22636X-RAY DIFFRACTION100
2.0927-2.1450.21321680.18292590X-RAY DIFFRACTION100
2.145-2.2030.23941260.17522659X-RAY DIFFRACTION100
2.203-2.26780.23211470.17982634X-RAY DIFFRACTION100
2.2678-2.3410.21871390.18442633X-RAY DIFFRACTION100
2.341-2.42470.22341430.17952624X-RAY DIFFRACTION100
2.4247-2.52170.20431410.1722656X-RAY DIFFRACTION100
2.5217-2.63650.18921340.16472653X-RAY DIFFRACTION100
2.6365-2.77550.2151480.17872658X-RAY DIFFRACTION100
2.7755-2.94930.17931250.1712691X-RAY DIFFRACTION100
2.9493-3.1770.21911390.16342684X-RAY DIFFRACTION100
3.177-3.49660.17881580.16462698X-RAY DIFFRACTION100
3.4966-4.00220.18741430.15282704X-RAY DIFFRACTION100
4.0022-5.04110.15321430.13452768X-RAY DIFFRACTION99
5.0411-43.09310.21341510.1692915X-RAY DIFFRACTION99

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