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- PDB-4zxz: Crystal structure of a highly thermal stable but inactive levoglu... -

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Basic information

Entry
Database: PDB / ID: 4zxz
TitleCrystal structure of a highly thermal stable but inactive levoglucosan kinase.
ComponentsLevoglucosan kinase
KeywordsDE NOVO PROTEIN / Transferase / sugar kinase.
Function / homologyATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Function and homology information
Biological speciesLipomyces starkeyi (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBacik, J.P. / Klesmith, J.R. / Whitehead, T.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1254238 United States
Department of Energy (DOE, United States) United States
CitationJournal: Acs Synth Biol / Year: 2015
Title: Comprehensive Sequence-Flux Mapping of a Levoglucosan Utilization Pathway in E. coli.
Authors: Klesmith, J.R. / Bacik, J.P. / Michalczyk, R. / Whitehead, T.A.
History
DepositionMay 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Dec 2, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 27, 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
B: Levoglucosan kinase


Theoretical massNumber of molelcules
Total (without water)98,9182
Polymers98,9182
Non-polymers00
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-23 kcal/mol
Surface area31500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.180, 88.950, 139.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Levoglucosan kinase


Mass: 49458.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lipomyces starkeyi (fungus) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Crystals were grown by mixing equal volumes of reservoir buffer containing 18% PEG3350 and 500 mM ammonium tartrate and the LGK construct at 21.5 mg/ml in crystallization buffer containing ...Details: Crystals were grown by mixing equal volumes of reservoir buffer containing 18% PEG3350 and 500 mM ammonium tartrate and the LGK construct at 21.5 mg/ml in crystallization buffer containing 20 mM Tris pH 7.5, 50 mM NaCl and 0.5 mM TCEP.

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→46.13 Å / Num. obs: 49339 / % possible obs: 90.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 6.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 1.6 / % possible all: 79

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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: 2.2→46.13 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2102 2505 5.08 %Random selection
Rwork0.1681 ---
obs0.1703 49264 90.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6640 0 0 394 7034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096788
X-RAY DIFFRACTIONf_angle_d1.1289215
X-RAY DIFFRACTIONf_dihedral_angle_d14.472505
X-RAY DIFFRACTIONf_chiral_restr0.0731028
X-RAY DIFFRACTIONf_plane_restr0.0061219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.24230.31891220.26562228X-RAY DIFFRACTION78
2.2423-2.28810.32571130.26132207X-RAY DIFFRACTION78
2.2881-2.33780.29971270.25352300X-RAY DIFFRACTION81
2.3378-2.39220.34881390.24882390X-RAY DIFFRACTION86
2.3922-2.4520.28451350.24562556X-RAY DIFFRACTION90
2.452-2.51830.28251510.24262657X-RAY DIFFRACTION94
2.5183-2.59240.29151530.22642709X-RAY DIFFRACTION96
2.5924-2.67610.24511360.2142744X-RAY DIFFRACTION96
2.6761-2.77170.26011440.21012738X-RAY DIFFRACTION96
2.7717-2.88270.24321510.18842682X-RAY DIFFRACTION95
2.8827-3.01390.25391260.19312767X-RAY DIFFRACTION95
3.0139-3.17270.25791400.17812723X-RAY DIFFRACTION94
3.1727-3.37140.20331470.16722687X-RAY DIFFRACTION94
3.3714-3.63170.19271620.1452675X-RAY DIFFRACTION93
3.6317-3.99690.15561400.1252687X-RAY DIFFRACTION93
3.9969-4.57490.14381260.11642683X-RAY DIFFRACTION92
4.5749-5.76210.1771450.12642653X-RAY DIFFRACTION90
5.7621-46.14270.14651480.1372673X-RAY DIFFRACTION87

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