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- PDB-6a8c: Ribokinase from Leishmania donovani with ADP -

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Basic information

Entry
Database: PDB / ID: 6a8c
TitleRibokinase from Leishmania donovani with ADP
ComponentsRibokinase
KeywordsTRANSFERASE / Nucleotide binding / ATP binding / Metal ion binding / Ribokinase activity / Carbohydrate metabolic process / cytoplasm
Function / homology
Function and homology information


ribokinase / ribokinase activity / D-ribose catabolic process / ATP binding / nucleus / metal ion binding / cytosol
Similarity search - Function
Ribokinase / Ribokinase/fructokinase / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase-like
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Ribokinase
Similarity search - Component
Biological speciesLeishmania donovani BPK282A1 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsGatreddi, S. / Vasudevan, D. / Qureshi, I.A.
CitationJournal: Int.J.Biol.Macromol. / Year: 2019
Title: Unraveling structural insights of ribokinase from Leishmania donovani.
Authors: Gatreddi, S. / Pillalamarri, V. / Vasudevan, D. / Addlagatta, A. / Qureshi, I.A.
History
DepositionJul 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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 / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribokinase
B: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,73024
Polymers75,1652
Non-polymers1,56522
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-199 kcal/mol
Surface area25550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.700, 100.700, 126.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ribokinase / RK


Mass: 37582.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani BPK282A1 (eukaryote)
Gene: LDBPK_270430 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: E9BIX7, ribokinase

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Non-polymers , 5 types, 318 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: 0.1M Citric acid, 3.4M Sodium chloride, 10mM Magnesium chloride, 9% Glycerol
PH range: 3.5-4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.98→51.14 Å / Num. obs: 50454 / % possible obs: 99.9 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 10.7
Reflection shellResolution: 1.98→2.03 Å / Rmerge(I) obs: 0.537 / Num. unique obs: 27089

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A8A

6a8a


Resolution: 1.98→51.14 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.575 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.141 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20924 2454 4.9 %RANDOM
Rwork0.16974 ---
obs0.17164 47960 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.973 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å2-0.39 Å2-0 Å2
2---0.77 Å20 Å2
3---2.51 Å2
Refinement stepCycle: 1 / Resolution: 1.98→51.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4892 0 84 296 5272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0145173
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174630
X-RAY DIFFRACTIONr_angle_refined_deg1.0381.6927059
X-RAY DIFFRACTIONr_angle_other_deg0.91.6510846
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3285672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.0622.687227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.18315822
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7091525
X-RAY DIFFRACTIONr_chiral_restr0.0550.2701
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025801
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02927
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_it2.0071.9772634
X-RAY DIFFRACTIONr_mcbond_other2.0071.9772633
X-RAY DIFFRACTIONr_mcangle_it2.8282.9553294
X-RAY DIFFRACTIONr_mcangle_other2.8282.9553295
X-RAY DIFFRACTIONr_scbond_it3.1412.3092539
X-RAY DIFFRACTIONr_scbond_other3.142.3082540
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6053.3273756
X-RAY DIFFRACTIONr_long_range_B_refined5.70724.245772
X-RAY DIFFRACTIONr_long_range_B_other5.70624.2395773
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 186 -
Rwork0.201 3525 -
obs--99.87 %

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