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- PDB-5knt: Crystal structure of E. coli hypoxanthine phosphoribosyltransfera... -

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Basic information

Entry
Database: PDB / ID: 5knt
TitleCrystal structure of E. coli hypoxanthine phosphoribosyltransferase in complexed with 2-((2,3-Dihydroxypropyl)(2-(hypoxanthin-9-yl)ethyl)amino)ethylphosphonic acid
ComponentsHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE/INHIBITOR / Acyclic nucleoside phosphonate / EcHPRT / phosphoribosyltransferase / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / guanosine tetraphosphate binding / protein homotetramerization ...hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / guanosine tetraphosphate binding / protein homotetramerization / nucleotide binding / magnesium ion binding / protein-containing complex / metal ion binding / identical protein binding / cytoplasm / cytosol
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-6WB / Hypoxanthine phosphoribosyltransferase / Hypoxanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,2736
Polymers41,2882
Non-polymers9854
Water3,549197
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)84,54612
Polymers82,5754
Non-polymers1,9708
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area8610 Å2
ΔGint-52 kcal/mol
Surface area27560 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-21 kcal/mol
Surface area15330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.655, 84.655, 166.819
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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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-6WB / 2-[[(2~{S})-2,3-bis(oxidanyl)propyl]-[2-(6-oxidanylidene-1~{H}-purin-9-yl)ethyl]amino]ethylphosphonic acid / 2-((2,3-Dihydroxypropyl)(2-(hypoxanthin-9-yl)ethyl)amino)ethylphosphonic acid


Mass: 361.291 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H20N5O6P
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 4.18 Å3/Da / Density % sol: 70.57 %
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: 2.55→44.3 Å / Num. obs: 23337 / % possible obs: 99.8 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 16.5

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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

1g9s


Resolution: 2.55→44.3 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.16
RfactorNum. reflection% reflection
Rfree0.217 1996 8.57 %
Rwork0.1662 --
obs0.1706 23286 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 154.54 Å2 / Biso mean: 51.9658 Å2 / Biso min: 23.62 Å2
Refinement stepCycle: final / Resolution: 2.55→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2686 0 81 198 2965
Biso mean--69.34 55.76 -
Num. residues----340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012853
X-RAY DIFFRACTIONf_angle_d1.1393851
X-RAY DIFFRACTIONf_chiral_restr0.041438
X-RAY DIFFRACTIONf_plane_restr0.005488
X-RAY DIFFRACTIONf_dihedral_angle_d13.5541122
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5478-2.61150.32721400.25011484162498
2.6115-2.68210.30521390.240614701609100
2.6821-2.7610.31751400.24415171657100
2.761-2.85010.30841380.226814961634100
2.8501-2.95190.30111360.218114871623100
2.9519-3.07010.28181440.223515161660100
3.0701-3.20980.28951470.204415011648100
3.2098-3.3790.27121430.182515121655100
3.379-3.59060.19751390.162315081647100
3.5906-3.86770.18121410.152115311672100
3.8677-4.25660.18291430.133115161659100
4.2566-4.87190.17261440.113815401684100
4.8719-6.13550.17831480.141715581706100
6.1355-44.31090.18591540.161716541808100

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