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- PDB-4zfv: Lipomyces starkeyi levoglucosan kinase bound to ADP and magnesium. -

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Basic information

Entry
Database: PDB / ID: 4zfv
TitleLipomyces starkeyi levoglucosan kinase bound to ADP and magnesium.
ComponentsLevoglucosan kinase
KeywordsTRANSFERASE / Sugar kinase / ATP-binding / carbohydrate metabolism
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: 1.5 Å
AuthorsBacik, J.P.
Funding support Canada, United States, 2items
OrganizationGrant numberCountry
Manitoba Health Research Council Canada
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
DepositionApr 21, 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 ...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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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
B: Levoglucosan kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,98810
Polymers98,7922
Non-polymers1,1968
Water25,9421440
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-73 kcal/mol
Surface area29330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.399, 114.399, 232.499
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1106-

HOH

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Components

#1: Protein Levoglucosan kinase


Mass: 49395.871 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)
References: UniProt: B3VI55, Transferases; Transferring phosphorus-containing groups
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / 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.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1440 / 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: 3.85 Å3/Da / Density % sol: 68.05 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Equal volumes of reservoir buffer (22% polyethylene glycol (PEG) 4000, 0.1 M sodium acetate, 0.1 M Tris pH 7.5) and LGK (7 mg/ml) in crystallization buffer (50 mM NaCl, 2 mM ADP, 4 mM MgCl2 ...Details: Equal volumes of reservoir buffer (22% polyethylene glycol (PEG) 4000, 0.1 M sodium acetate, 0.1 M Tris pH 7.5) and LGK (7 mg/ml) in crystallization buffer (50 mM NaCl, 2 mM ADP, 4 mM MgCl2 , 0.5 mM TCEP, 20 mM Tris pH 7.5) were mixed.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→47.2 Å / Num. obs: 244767 / % possible obs: 99.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 10.3
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

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

4yh5


Resolution: 1.5→47.2 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1742 12339 5.04 %
Rwork0.1576 --
obs0.1584 244650 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6712 0 74 1440 8226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077056
X-RAY DIFFRACTIONf_angle_d1.0959637
X-RAY DIFFRACTIONf_dihedral_angle_d13.2672654
X-RAY DIFFRACTIONf_chiral_restr0.0721057
X-RAY DIFFRACTIONf_plane_restr0.0051288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5170.26854010.25267688X-RAY DIFFRACTION100
1.517-1.53490.25683820.23757652X-RAY DIFFRACTION100
1.5349-1.55360.27464090.23087676X-RAY DIFFRACTION100
1.5536-1.57330.24694190.21987689X-RAY DIFFRACTION100
1.5733-1.5940.24324210.21847664X-RAY DIFFRACTION100
1.594-1.61580.23554430.20427617X-RAY DIFFRACTION100
1.6158-1.63890.20864290.20227690X-RAY DIFFRACTION100
1.6389-1.66340.20833900.19127661X-RAY DIFFRACTION100
1.6634-1.68940.20643880.18427681X-RAY DIFFRACTION100
1.6894-1.71710.19224080.187711X-RAY DIFFRACTION100
1.7171-1.74670.19814120.17897693X-RAY DIFFRACTION100
1.7467-1.77840.18924140.17227679X-RAY DIFFRACTION100
1.7784-1.81260.17194170.16397713X-RAY DIFFRACTION100
1.8126-1.84960.17424270.15937671X-RAY DIFFRACTION100
1.8496-1.88990.16964070.15987698X-RAY DIFFRACTION100
1.8899-1.93380.15654090.15737718X-RAY DIFFRACTION100
1.9338-1.98220.16884060.15947720X-RAY DIFFRACTION100
1.9822-2.03580.17274070.14857725X-RAY DIFFRACTION100
2.0358-2.09570.17394070.15067762X-RAY DIFFRACTION100
2.0957-2.16330.17714080.14837746X-RAY DIFFRACTION100
2.1633-2.24060.15154070.14537750X-RAY DIFFRACTION100
2.2406-2.33040.16514100.14457764X-RAY DIFFRACTION100
2.3304-2.43640.17144090.14667769X-RAY DIFFRACTION100
2.4364-2.56490.15694100.14837796X-RAY DIFFRACTION100
2.5649-2.72550.16874120.14747816X-RAY DIFFRACTION100
2.7255-2.93590.16434110.14927826X-RAY DIFFRACTION100
2.9359-3.23130.16024140.14887852X-RAY DIFFRACTION100
3.2313-3.69880.16174170.1417899X-RAY DIFFRACTION100
3.6988-4.65940.13974140.13047912X-RAY DIFFRACTION99
4.6594-47.22610.17724310.16058073X-RAY DIFFRACTION97

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