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- PDB-4jls: Crystal Structure of E. coli XGPRT in complex with (3R,4S)-4-(Gua... -

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Basic information

Entry
Database: PDB / ID: 4jls
TitleCrystal Structure of E. coli XGPRT in complex with (3R,4S)-4-(Guanin-9-yl)-3-hydroxypyrrolidin-1-N-ylacetylphosphonic acid
ComponentsXanthine phosphoribosyltransferase
KeywordsTRANSFERASE / XANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE / PURINE SALVAGE / NUCLEOSIDE PHOSPHONATE / ANTIBACTERIAL
Function / homologyRossmann fold - #2020 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Chem-3ZE / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKeough, D.T. / Hockova, D. / Rejman, D. / Spacek, P. / Vrbkova, S. / Krecmerova, M. / Eng, W.S. / Jans, H. / West, N.P. / Naesens, L.M.J. ...Keough, D.T. / Hockova, D. / Rejman, D. / Spacek, P. / Vrbkova, S. / Krecmerova, M. / Eng, W.S. / Jans, H. / West, N.P. / Naesens, L.M.J. / de Jersey, J. / Guddat, L.W.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Inhibition of the Escherichia coli 6-oxopurine phosphoribosyltransferases by nucleoside phosphonates: potential for new antibacterial agents.
Authors: Keough, D.T. / Hockova, D. / Rejman, D. / Spacek, P. / Vrbkova, S. / Krecmerova, M. / Eng, W.S. / Jans, H. / West, N.P. / Naesens, L.M. / de Jersey, J. / Guddat, L.W.
History
DepositionMar 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xanthine phosphoribosyltransferase
B: Xanthine phosphoribosyltransferase
C: Xanthine phosphoribosyltransferase
D: Xanthine phosphoribosyltransferase
E: Xanthine phosphoribosyltransferase
H: Xanthine phosphoribosyltransferase
I: Xanthine phosphoribosyltransferase
J: Xanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,79916
Polymers135,9338
Non-polymers2,8668
Water8,269459
1
A: Xanthine phosphoribosyltransferase
B: Xanthine phosphoribosyltransferase
C: Xanthine phosphoribosyltransferase
D: Xanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3998
Polymers67,9664
Non-polymers1,4334
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10680 Å2
ΔGint-48 kcal/mol
Surface area21830 Å2
MethodPISA
2
E: Xanthine phosphoribosyltransferase
H: Xanthine phosphoribosyltransferase
I: Xanthine phosphoribosyltransferase
J: Xanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3998
Polymers67,9664
Non-polymers1,4334
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10560 Å2
ΔGint-52 kcal/mol
Surface area21130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.610, 117.679, 156.622
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Xanthine phosphoribosyltransferase / / Xanthine-guanine phosphoribosyltransferase


Mass: 16991.568 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: str. K-12 substr. MDS42 / Gene: gpt, ECMDS42_0227 / Production host: Escherichia coli (E. coli)
References: UniProt: H0Q6L9, xanthine phosphoribosyltransferase
#2: Chemical
ChemComp-3ZE / {2-[(3S,4R)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-4-hydroxypyrrolidin-1-yl]-2-oxoethyl}phosphonic acid


Mass: 358.247 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H15N6O6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: 8% tacsimate, pH 6.0, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 6, 2011
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 71529 / Num. obs: 71529 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.2549 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.971 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 23.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2204 2000 2.8 %random
Rwork0.1774 ---
obs0.1884 71529 99.97 %-
all-71529 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→19.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8183 0 192 459 8834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088591
X-RAY DIFFRACTIONf_angle_d1.17111757
X-RAY DIFFRACTIONf_dihedral_angle_d15.2123157
X-RAY DIFFRACTIONf_chiral_restr0.0691310
X-RAY DIFFRACTIONf_plane_restr0.0051472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.25490.30831410.25664925X-RAY DIFFRACTION100
2.2549-2.31580.28341410.23624877X-RAY DIFFRACTION100
2.3158-2.38390.29081410.23464916X-RAY DIFFRACTION100
2.3839-2.46070.26031420.22274916X-RAY DIFFRACTION100
2.4607-2.54850.28161410.214908X-RAY DIFFRACTION100
2.5485-2.65030.21661410.20324911X-RAY DIFFRACTION100
2.6503-2.77060.29431420.21674930X-RAY DIFFRACTION100
2.7706-2.91620.27421430.22234976X-RAY DIFFRACTION100
2.9162-3.09830.30931420.21674925X-RAY DIFFRACTION100
3.0983-3.33650.26181430.20324980X-RAY DIFFRACTION100
3.3365-3.67040.20521430.18254958X-RAY DIFFRACTION100
3.6704-4.19730.20221450.15845029X-RAY DIFFRACTION100
4.1973-5.2720.20961450.15195042X-RAY DIFFRACTION100
5.272-19.97170.18331500.16265236X-RAY DIFFRACTION100

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