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- PDB-4jit: Crystal Structure of E. coli XGPRT in complex with (S)-3-(Guanin-... -

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Basic information

Entry
Database: PDB / ID: 4jit
TitleCrystal Structure of E. coli XGPRT in complex with (S)-3-(Guanin-9-yl)pyrrolidin-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-3ZF / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 7, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6516
Polymers67,9664
Non-polymers6842
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11220 Å2
ΔGint-60 kcal/mol
Surface area24330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.066, 94.066, 162.633
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Xanthine phosphoribosyltransferase / Xanthine-guanine phosphoribosyltransferase


Mass: 16991.568 Da / Num. of mol.: 4
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-3ZF / {2-[(3S)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)pyrrolidin-1-yl]-2-oxoethyl}phosphonic acid


Mass: 342.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N6O5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.65 Å3/Da / Density % sol: 53.53 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: 8% tacsimate, pH 7.0, 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: 2.8→20 Å / Num. all: 18634 / Num. obs: 18634 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.8→2.8756 Å / % possible all: 99.7

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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: 2.8→19.87 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 29.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2642 928 10 %random
Rwork0.2076 ---
obs0.2133 18569 99.92 %-
all-18569 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4511 0 46 2 4559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044669
X-RAY DIFFRACTIONf_angle_d0.866383
X-RAY DIFFRACTIONf_dihedral_angle_d14.021679
X-RAY DIFFRACTIONf_chiral_restr0.054722
X-RAY DIFFRACTIONf_plane_restr0.003817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.87560.36591380.31011247X-RAY DIFFRACTION100
2.8756-2.960.33071430.27391278X-RAY DIFFRACTION100
2.96-3.05520.31411380.24941250X-RAY DIFFRACTION100
3.0552-3.16390.30291400.24331258X-RAY DIFFRACTION100
3.1639-3.29010.28491410.24091269X-RAY DIFFRACTION100
3.2901-3.43910.31741390.24111243X-RAY DIFFRACTION100
3.4391-3.61940.30031430.22931302X-RAY DIFFRACTION100
3.6194-3.84460.22841400.20981252X-RAY DIFFRACTION100
3.8446-4.1390.26061430.19641295X-RAY DIFFRACTION100
4.139-4.5510.23631420.18081276X-RAY DIFFRACTION100
4.551-5.19920.25511460.19231313X-RAY DIFFRACTION100
5.1992-6.51190.28651470.21141327X-RAY DIFFRACTION100
6.5119-19.87090.22171560.17251403X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -24.3803 Å / Origin y: 24.8837 Å / Origin z: -2.2408 Å
111213212223313233
T0.3744 Å20.02 Å2-0.0326 Å2-0.4091 Å20.0456 Å2--0.5581 Å2
L1.1473 °20.0194 °20.1228 °2-1.6511 °20.7866 °2--4.3733 °2
S0.0478 Å °-0.3061 Å °-0.0922 Å °0.1975 Å °0.1827 Å °-0.0604 Å °0.1808 Å °-0.0605 Å °-0.2462 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:151 ) OR ( CHAIN C AND ( RESID 3:152 OR RESID 201:201 OR RESID 301:301 ) ) OR ( CHAIN B AND ( RESID 3:152 OR RESID 201:201 OR RESID 301:301 ) ) OR ( CHAIN D AND RESID 3:152 )A3 - 151
2X-RAY DIFFRACTION1( CHAIN A AND RESID 3:151 ) OR ( CHAIN C AND ( RESID 3:152 OR RESID 201:201 OR RESID 301:301 ) ) OR ( CHAIN B AND ( RESID 3:152 OR RESID 201:201 OR RESID 301:301 ) ) OR ( CHAIN D AND RESID 3:152 )C3 - 152
3X-RAY DIFFRACTION1( CHAIN A AND RESID 3:151 ) OR ( CHAIN C AND ( RESID 3:152 OR RESID 201:201 OR RESID 301:301 ) ) OR ( CHAIN B AND ( RESID 3:152 OR RESID 201:201 OR RESID 301:301 ) ) OR ( CHAIN D AND RESID 3:152 )C201
4X-RAY DIFFRACTION1( CHAIN A AND RESID 3:151 ) OR ( CHAIN C AND ( RESID 3:152 OR RESID 201:201 OR RESID 301:301 ) ) OR ( CHAIN B AND ( RESID 3:152 OR RESID 201:201 OR RESID 301:301 ) ) OR ( CHAIN D AND RESID 3:152 )C301
5X-RAY DIFFRACTION1( CHAIN A AND RESID 3:151 ) OR ( CHAIN C AND ( RESID 3:152 OR RESID 201:201 OR RESID 301:301 ) ) OR ( CHAIN B AND ( RESID 3:152 OR RESID 201:201 OR RESID 301:301 ) ) OR ( CHAIN D AND RESID 3:152 )B3 - 152
6X-RAY DIFFRACTION1( CHAIN A AND RESID 3:151 ) OR ( CHAIN C AND ( RESID 3:152 OR RESID 201:201 OR RESID 301:301 ) ) OR ( CHAIN B AND ( RESID 3:152 OR RESID 201:201 OR RESID 301:301 ) ) OR ( CHAIN D AND RESID 3:152 )B201
7X-RAY DIFFRACTION1( CHAIN A AND RESID 3:151 ) OR ( CHAIN C AND ( RESID 3:152 OR RESID 201:201 OR RESID 301:301 ) ) OR ( CHAIN B AND ( RESID 3:152 OR RESID 201:201 OR RESID 301:301 ) ) OR ( CHAIN D AND RESID 3:152 )B301
8X-RAY DIFFRACTION1( CHAIN A AND RESID 3:151 ) OR ( CHAIN C AND ( RESID 3:152 OR RESID 201:201 OR RESID 301:301 ) ) OR ( CHAIN B AND ( RESID 3:152 OR RESID 201:201 OR RESID 301:301 ) ) OR ( CHAIN D AND RESID 3:152 )D3 - 152

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