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- PDB-8cqx: Ribokinase from T.sp mutant A92G -

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Basic information

Entry
Database: PDB / ID: 8cqx
TitleRibokinase from T.sp mutant A92G
ComponentsRibokinase
KeywordsHYDROLASE / mutant / ribokinase
Function / homology
Function and homology information


ribokinase / ribokinase activity / D-ribose catabolic process / ATP binding / metal ion binding / cytosol
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 / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase ...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 / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Ribokinase
Similarity search - Component
Biological speciesThermus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsTimofeev, V.I. / Shevtsov, M.B. / Abramchik, Y.A. / Kostromina, M.A. / Zayats, E.A. / Kuranova, I.P. / Esipov, R.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Ribokinase from T.sp mutant A92G
Authors: Timofeev, V.I. / Shevtsov, M.B. / Abramchik, Y.A. / Kostromina, M.A. / Zayats, E.A. / Kuranova, I.P. / Esipov, R.S.
History
DepositionMar 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)125,83111
Polymers124,0504
Non-polymers1,7827
Water3,639202
1
A: Ribokinase
D: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9045
Polymers62,0252
Non-polymers8793
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-34 kcal/mol
Surface area22860 Å2
MethodPISA
2
B: Ribokinase
hetero molecules

C: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9286
Polymers62,0252
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area3930 Å2
ΔGint-33 kcal/mol
Surface area24090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.307, 155.608, 82.915
Angle α, β, γ (deg.)90.00, 96.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ribokinase


Mass: 31012.416 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus sp. (bacteria) / Gene: rbsK / Production host: Thermus sp. (bacteria) / References: UniProt: A0A0B0SD75
#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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% peg3350, 0,45 M NaCl, 0,1 M citric acid pH 5.0, 5 mM MgCl2, 5 mM ADP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER R 1M / Detector: PIXEL / Date: Sep 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.27→30 Å / Num. obs: 51152 / % possible obs: 99.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.133 / Rrim(I) all: 0.158 / Net I/σ(I): 3.886
Reflection shellResolution: 2.27→2.39 Å / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 25537

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Processing

Software
NameVersionClassification
REFMAC5refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→29.52 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.844 / SU B: 10.246 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R: 0.454 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31148 2481 4.9 %RANDOM
Rwork0.22932 ---
obs0.23322 48607 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.734 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.02 Å2
2---0.01 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.27→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8732 0 111 202 9045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0139012
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158873
X-RAY DIFFRACTIONr_angle_refined_deg1.671.6412313
X-RAY DIFFRACTIONr_angle_other_deg1.2391.56920321
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.00251198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.54221.442430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.244151359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6531577
X-RAY DIFFRACTIONr_chiral_restr0.0670.21173
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210427
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021971
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_it3.4163.9314801
X-RAY DIFFRACTIONr_mcbond_other3.4123.934799
X-RAY DIFFRACTIONr_mcangle_it5.2855.8845996
X-RAY DIFFRACTIONr_mcangle_other5.2825.8845996
X-RAY DIFFRACTIONr_scbond_it3.464.3944211
X-RAY DIFFRACTIONr_scbond_other3.4584.3944211
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4756.456318
X-RAY DIFFRACTIONr_long_range_B_refined8.46547.6769392
X-RAY DIFFRACTIONr_long_range_B_other8.46347.6919380
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.27→2.329 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 186 -
Rwork0.287 3643 -
obs--99.56 %

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