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- PDB-5kns: E coli hypoxanthine guanine phosphoribosyltransferase in complexe... -

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Basic information

Entry
Database: PDB / ID: 5kns
TitleE coli hypoxanthine guanine phosphoribosyltransferase in complexed with 9-[(N-phosphonoethyl-N-phosphonoethoxyethyl)-2-aminoethyl]hypoxanthine
ComponentsHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE/INHIBITOR / Acyclic nucleoside phosphonate / EcHPRT / 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-3L7 / Hypoxanthine phosphoribosyltransferase / Hypoxanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.792 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 1.1Mar 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)42,6888
Polymers41,2882
Non-polymers1,4006
Water3,063170
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)85,37516
Polymers82,5754
Non-polymers2,80012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area9700 Å2
ΔGint-46 kcal/mol
Surface area27570 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-19 kcal/mol
Surface area15440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.411, 84.411, 167.140
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
11A-347-

HOH

21B-328-

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-3L7 / (2-{[2-(6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl](2-{[(E)-2-phosphonoethenyl]oxy}ethyl)amino}ethyl)phosphonic acid


Mass: 437.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H21N5O8P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 4.27 Å3/Da / Density % sol: 71.2 %
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: 2.79→44.311 Å / Num. obs: 17769 / % possible obs: 99.8 % / Redundancy: 10.8 % / Net I/σ(I): 18

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 2.792→44.311 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.7
RfactorNum. reflection% reflection
Rfree0.2095 1770 9.99 %
Rwork0.1553 --
obs0.1607 17724 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 198.3 Å2 / Biso mean: 62.3995 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.792→44.311 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2697 0 88 170 2955
Biso mean--119.85 62.57 -
Num. residues----341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042888
X-RAY DIFFRACTIONf_angle_d0.6273887
X-RAY DIFFRACTIONf_chiral_restr0.02440
X-RAY DIFFRACTIONf_plane_restr0.002488
X-RAY DIFFRACTIONf_dihedral_angle_d12.1611105
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7923-2.86780.35971310.26291189132099
2.8678-2.95220.2791330.228711961329100
2.9522-3.04740.24941350.198212141349100
3.0474-3.15630.2451340.191712031337100
3.1563-3.28270.27831380.192912171355100
3.2827-3.4320.221310.163512031334100
3.432-3.61290.23471310.153412121343100
3.6129-3.83910.21181360.144712441380100
3.8391-4.13530.17261320.133512051337100
4.1353-4.55110.16961390.119812401379100
4.5511-5.20880.16321370.120212411378100
5.2088-6.55910.19611430.160912601403100
6.5591-44.31690.20691500.15741330148099
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.2958-0.8842-0.96832.55751.31013.6438-0.0333-0.1219-0.016-0.04430.04920.2840.0646-0.30470.01450.2529-0.08720.01880.580.04820.3946-33.2534.2579-38.4875
22.5552-0.29570.36912.9872-0.75872.8063-0.084-0.0876-0.0039-0.14160.1341-0.2520.01220.3329-0.02790.229-0.06510.01310.5747-0.02950.3666-10.515436.2535-37.0613
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 4 through 180)A4 - 180
2X-RAY DIFFRACTION2(chain 'B' and resid 4 through 181)B4 - 181

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