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- PDB-6znx: Ribokinase from Thermus Species -

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Basic information

Entry
Database: PDB / ID: 6znx
TitleRibokinase from Thermus Species
ComponentsRibokinase
KeywordsTRANSFERASE / ADP
Function / homology
Function and homology information


ribokinase / ribokinase activity / D-ribose catabolic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Ribokinase / Ribokinase/fructokinase / pfkB family of carbohydrate kinases signature 1. / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase-like
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Ribokinase
Similarity search - Component
Biological speciesThermus sp. 2.9 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTimofeev, V.I. / Abramchik, Y.A. / Tuzova, E.S. / Esipova, L.V. / Mikheeva, O.O. / Kostromina, M.A. / Kuranova, I.P. / Esipov, R.S.
CitationJournal: To Be Published
Title: Ribokinase from Thermus Species
Authors: Timofeev, V.I. / Abramchik, Y.A. / Tuzova, E.S. / Esipova, L.V. / Mikheeva, O.O. / Kostromina, M.A. / Kuranova, I.P. / Esipov, R.S.
History
DepositionJul 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribokinase
B: Ribokinase
C: Ribokinase
D: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,8158
Polymers124,1064
Non-polymers1,7094
Water3,351186
1
A: Ribokinase
hetero molecules

D: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9074
Polymers62,0532
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
Buried area3810 Å2
ΔGint-29 kcal/mol
Surface area22980 Å2
MethodPISA
2
B: Ribokinase
hetero molecules

C: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9074
Polymers62,0532
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area3410 Å2
ΔGint-30 kcal/mol
Surface area23140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.210, 155.550, 83.040
Angle α, β, γ (deg.)90.000, 98.200, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ribokinase / RK


Mass: 31026.439 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus sp. 2.9 (bacteria) / Gene: rbsK, QT17_05185 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B0SD75, ribokinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.28 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 293 K / Method: counter-diffusion / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 41928 / % possible obs: 96.91 % / Redundancy: 3.18 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 5.2958
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.28 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 4.47 / Num. unique obs: 6150 / % possible all: 97.73

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XDA

4xda


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.882 / SU B: 9.44 / SU ML: 0.224 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.697 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.271 2072 5 %RANDOM
Rwork0.2274 ---
obs0.2295 39758 96.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.21 Å2 / Biso mean: 36.213 Å2 / Biso min: 3.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.45 Å2-0 Å22.35 Å2
2---5.23 Å2-0 Å2
3---2.02 Å2
Refinement stepCycle: final / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8259 0 108 186 8553
Biso mean--42.54 31.62 -
Num. residues----1138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0138500
X-RAY DIFFRACTIONr_bond_other_d0.0030.0178201
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.63511588
X-RAY DIFFRACTIONr_angle_other_deg1.2021.56618912
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.55951119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18621.787403
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.61151273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2861568
X-RAY DIFFRACTIONr_chiral_restr0.0650.21108
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029646
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021654
LS refinement shellResolution: 2.4→2.461 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 139 -
Rwork0.25 2939 -
all-3078 -
obs--97.07 %

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