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

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Basic information

Entry
Database: PDB / ID: 5knu
TitleCrystal structure of E. coli hypoxanthine phosphoribosyltransferase in complexed with 9-[N,N-(Bis-3-phosphonopropyl)aminomethyl]-9-deazahypoxanthine
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-6WA / Hypoxanthine phosphoribosyltransferase / Hypoxanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.808 Å
AuthorsEng, W.S. / Keough, D.T. / Baszczynski, O. / 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.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)42,3917
Polymers41,2882
Non-polymers1,1035
Water1,18966
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)84,78214
Polymers82,5754
Non-polymers2,20710
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area9130 Å2
ΔGint-69 kcal/mol
Surface area28330 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-30 kcal/mol
Surface area15800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.975, 84.975, 167.723
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-316-

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-6WA / 3-[(4-oxidanylidene-3,5-dihydropyrrolo[3,2-d]pyrimidin-7-yl)methyl-(3-phosphonopropyl)amino]propylphosphonic acid / 9-[N,N-(Bis-3-phosphonopropyl)aminomethyl]-9-deazahypoxanthine


Mass: 408.284 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H22N4O7P2
#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


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.: 66 / 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: 4.23 Å3/Da / Density % sol: 70.95 %
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: 2.808→44.52 Å / Num. obs: 17700 / % possible obs: 99.5 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 0.997

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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: 2.808→44.518 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.59
RfactorNum. reflection% reflection
Rfree0.2213 1746 9.89 %
Rwork0.1758 --
obs0.1804 17655 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 146.28 Å2 / Biso mean: 42.1829 Å2 / Biso min: 12.73 Å2
Refinement stepCycle: final / Resolution: 2.808→44.518 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2706 0 69 66 2841
Biso mean--79.02 43.95 -
Num. residues----345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052871
X-RAY DIFFRACTIONf_angle_d0.6363863
X-RAY DIFFRACTIONf_chiral_restr0.022441
X-RAY DIFFRACTIONf_plane_restr0.002486
X-RAY DIFFRACTIONf_dihedral_angle_d12.2561108
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 (%)
2.8079-2.89050.34711330.25231238137194
2.8905-2.98370.31491440.232813001444100
2.9837-3.09040.26491420.224912951437100
3.0904-3.21410.28131460.230813171463100
3.2141-3.36030.24221480.201613231471100
3.3603-3.53740.21091400.176713091449100
3.5374-3.75890.30041460.22113141460100
3.7589-4.04890.19821440.163613311475100
4.0489-4.45610.17261450.133513471492100
4.4561-5.10010.17461470.133113401487100
5.1001-6.42250.21241510.157613551506100
6.4225-44.52330.17871600.157614401600100

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