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- PDB-6vwo: Crystal structure of E. coli guanosine kinase -

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Basic information

Entry
Database: PDB / ID: 6vwo
TitleCrystal structure of E. coli guanosine kinase
ComponentsInosine-guanosine kinase
KeywordsTRANSFERASE / Guanosine Kinase
Function / homology
Function and homology information


guanosine kinase activity / inosine kinase / inosine kinase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / guanosine tetraphosphate binding / phosphorylation / ATP binding
Similarity search - Function
Guanosine-inosine kinase / 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 / GUANOSINE / : / Guanosine-inosine kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å
AuthorsWang, B. / Grant, R.A. / Laub, M.T.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM082899 United States
CitationJournal: Mol.Cell / Year: 2020
Title: ppGpp Coordinates Nucleotide and Amino-Acid Synthesis in E. coli During Starvation.
Authors: Wang, B. / Grant, R.A. / Laub, M.T.
History
DepositionFeb 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inosine-guanosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9208
Polymers48,7851
Non-polymers1,1357
Water3,675204
1
A: Inosine-guanosine kinase
hetero molecules

A: Inosine-guanosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,84016
Polymers97,5702
Non-polymers2,27114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Unit cell
Length a, b, c (Å)118.117, 118.117, 75.447
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-504-

K

21A-760-

HOH

31A-773-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Inosine-guanosine kinase


Mass: 48784.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: gsk, b0477, JW0466 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEW6, inosine kinase

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Non-polymers , 5 types, 211 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-GMP / GUANOSINE / Guanosine


Mass: 283.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O5
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.11 Å3/Da / Density % sol: 60.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.9 / Details: 0.1 M TRIS pH 8.9, 15% PEG-4000, 0.2M CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 55162 / % possible obs: 95 % / Redundancy: 16.6 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.02 / Rrim(I) all: 0.086 / Χ2: 1.022 / Net I/σ(I): 6.6 / Num. measured all: 918133
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.815.20.89614170.7320.3810.9790.4349
1.81-1.846.30.81219270.8460.30.870.45166.7
1.84-1.887.20.76424370.830.2610.8120.47385.6
1.88-1.928.80.81627960.8010.2640.8620.53897.3
1.92-1.9611.60.78928790.8960.2310.8240.48499.8
1.96-214.50.71528870.950.1910.740.499100
2-2.0516.40.57928760.9720.1460.5980.512100
2.05-2.1116.50.51528800.9710.1290.5310.57100
2.11-2.1719.40.43528830.9830.1010.4470.564100
2.17-2.24200.35828760.9890.0820.3680.62100
2.24-2.3219.80.29328920.9910.0680.3010.677100
2.32-2.4219.70.23128990.9940.0530.2370.725100
2.42-2.5318.50.18328960.9950.0440.1880.85100
2.53-2.6619.10.14229020.9970.0330.1460.964100
2.66-2.8320.50.12428980.9980.0280.1271.128100
2.83-3.0420.10.09929250.9980.0230.1021.325100
3.04-3.3518.50.08129350.9980.0190.0831.636100
3.35-3.8320.70.06929170.9990.0150.071.97399.9
3.83-4.8319.40.05329670.9990.0120.0542.001100
4.83-5019.10.04830730.9990.0110.0491.708100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ensemble

Resolution: 1.78→46.5 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.87
RfactorNum. reflection% reflection
Rfree0.2048 4244 7.7 %
Rwork0.1806 --
obs0.1825 55093 94.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.89 Å2 / Biso mean: 46.0518 Å2 / Biso min: 21.22 Å2
Refinement stepCycle: final / Resolution: 1.78→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2973 0 108 204 3285
Biso mean--44.55 45.04 -
Num. residues----383
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.78-1.80.3226750.330785693149
1.8-1.830.317920.31541044113658
1.83-1.850.31541000.31591236133669
1.85-1.870.36581210.30851458157983
1.87-1.90.35471390.28991637177692
1.9-1.920.32261450.28481720186599
1.92-1.950.29641450.25617771922100
1.95-1.980.30281440.248117551899100
1.98-2.010.24021510.236817701921100
2.01-2.040.21811480.211317631911100
2.04-2.080.27711460.213817571903100
2.08-2.110.241450.209817921937100
2.11-2.160.2141510.201518091960100
2.16-2.20.2241410.192917261867100
2.2-2.250.21831490.194117781927100
2.25-2.30.25371500.191717851935100
2.3-2.360.21851430.195317461889100
2.36-2.420.24161520.187617941946100
2.42-2.490.22591470.178317631910100
2.49-2.570.20441570.188817931950100
2.57-2.660.21271490.183317681917100
2.66-2.770.19091450.1818021947100
2.77-2.90.23331510.19117851936100
2.9-3.050.21321440.190917831927100
3.05-3.240.21211530.187217961949100
3.24-3.490.22911480.174318121960100
3.49-3.840.19021430.171217941937100
3.84-4.40.15121530.136818261979100
4.4-5.540.1511540.134918241978100
5.54-46.50.18361630.179319002063100

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