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- PDB-5knr: E. coli HPRT in complexed with 9-[(N-phosphonoethyl-N-phosphonoet... -

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Basic information

Entry
Database: PDB / ID: 5knr
TitleE. coli HPRT in complexed with 9-[(N-phosphonoethyl-N-phosphonoethoxyethyl)-2-aminoethyl]-guanine
ComponentsHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE/INHIBITOR / Inhibitor / complex / phosphoribosyltransferase / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase / GMP salvage / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / purine ribonucleoside salvage / guanosine tetraphosphate binding / protein homotetramerization ...guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase / GMP salvage / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / purine ribonucleoside salvage / guanosine tetraphosphate binding / protein homotetramerization / nucleotide binding / magnesium ion binding / protein-containing complex / metal ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Hypoxanthine phosphoribosyl transferase / Purine/pyrimidine phosphoribosyl transferases signature. / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3L5 / Hypoxanthine phosphoribosyltransferase / Hypoxanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.864 Å
AuthorsEng, W.S. / Keough, D.T. / Hockova, D. / Janeba, Z.
CitationJournal: Chemistryselect / Year: 2016
Title: Crystal Structures of Acyclic Nucleoside Phosphonates in Complex with Escherichia coli Hypoxanthine Phosphoribosyltransferase
Authors: Eng, W.S. / Hockova, D. / Spacek, P. / Baszczynski, O. / Janeba, Z. / Naesens, L. / Keough, D.T. / Guddat, L.W.
History
DepositionJun 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypoxanthine-guanine phosphoribosyltransferase
B: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2215
Polymers41,2882
Non-polymers9333
Water43224
1
A: Hypoxanthine-guanine phosphoribosyltransferase
B: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules

A: Hypoxanthine-guanine phosphoribosyltransferase
B: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,44110
Polymers82,5754
Non-polymers1,8666
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-25 kcal/mol
Surface area15230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.617, 84.617, 167.116
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-307-

HOH

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Components

#1: Protein Hypoxanthine-guanine phosphoribosyltransferase /


Mass: 20643.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hpt, ACN002_0124 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U4JN50, UniProt: P0A9M2*PLUS
#2: Chemical ChemComp-3L5 / (2-{[2-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)ethyl][2-(2-phosphonoethoxy)ethyl]amino}ethyl)phosphonic acid


Mass: 454.313 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H24N6O8P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 24 / 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: 4.14 Å3/Da / Density % sol: 70.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.5 and 0.1 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.86→44.35 Å / Num. obs: 16596 / % possible obs: 99.9 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 15.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G9S
Resolution: 2.864→44.347 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.51
RfactorNum. reflection% reflection
Rfree0.2671 1660 10.08 %
Rwork0.2329 --
obs0.2364 16465 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 209.87 Å2 / Biso mean: 55.0857 Å2 / Biso min: 21.73 Å2
Refinement stepCycle: final / Resolution: 2.864→44.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2680 0 59 24 2763
Biso mean--89.57 50.46 -
Num. residues----342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022805
X-RAY DIFFRACTIONf_angle_d0.583783
X-RAY DIFFRACTIONf_chiral_restr0.021434
X-RAY DIFFRACTIONf_plane_restr0.003474
X-RAY DIFFRACTIONf_dihedral_angle_d12.2981087
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.864-2.94830.36911360.321216135299
2.9483-3.04340.31711370.282812241361100
3.0434-3.15220.31251370.272812021339100
3.1522-3.27830.33441340.275612391373100
3.2783-3.42750.27771370.24111961333100
3.4275-3.60810.3281320.26831208134098
3.6081-3.83410.27711340.27871226136098
3.8341-4.12990.36831340.29931187132198
4.1299-4.54510.231370.186812451382100
4.5451-5.20190.19641420.169812601402100
5.2019-6.55050.23741430.198612691412100
6.5505-44.35220.1841570.186613331490100

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