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- PDB-6a8b: Ribokinase from Leishmania donovani with AMPPCP -

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Basic information

Entry
Database: PDB / ID: 6a8b
TitleRibokinase from Leishmania donovani with AMPPCP
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 / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Ribokinase / Ribokinase/fructokinase / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Ribokinase
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsGatreddi, S. / Pillalamarri, V. / 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribokinase
B: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,83820
Polymers75,1652
Non-polymers1,67318
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-162 kcal/mol
Surface area24950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.395, 100.395, 125.785
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 (eukaryote) / Strain: BPK282A1 / 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, 192 molecules

#2: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.44 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: 0.1M Citric acid pH 4.3, 3.4M Sodium chloride, 10mM Magnesium chloride, 10% Glycerol
PH range: 3.5-4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU AFC-5R / Detector: CCD / Date: Jan 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.01→31.79 Å / Num. obs: 47985 / % possible obs: 99.9 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 14.9
Reflection shellResolution: 2.01→2.06 Å / Rmerge(I) obs: 0.661 / Num. unique obs: 3514

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A8A

6a8a


Resolution: 2.01→31.79 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.167 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22592 2431 5.1 %RANDOM
Rwork0.18394 ---
obs0.18604 45514 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.735 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å2-0.63 Å2-0 Å2
2---1.26 Å20 Å2
3---4.09 Å2
Refinement stepCycle: 1 / Resolution: 2.01→31.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4856 0 92 174 5122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135039
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174596
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.6636866
X-RAY DIFFRACTIONr_angle_other_deg1.3691.57510661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0415656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.59722.727220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4715779
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3031524
X-RAY DIFFRACTIONr_chiral_restr0.0730.2681
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025680
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02998
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_it2.3492.9392618
X-RAY DIFFRACTIONr_mcbond_other2.3462.9392617
X-RAY DIFFRACTIONr_mcangle_it3.3264.3963270
X-RAY DIFFRACTIONr_mcangle_other3.3264.3973271
X-RAY DIFFRACTIONr_scbond_it3.0853.3122421
X-RAY DIFFRACTIONr_scbond_other3.0843.3112422
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6164.8343595
X-RAY DIFFRACTIONr_long_range_B_refined6.09635.6765456
X-RAY DIFFRACTIONr_long_range_B_other6.09835.6645442
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.006→2.058 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 209 -
Rwork0.245 3275 -
obs--99.97 %

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