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- PDB-1g9s: CRYSTAL STRUCTURE OF A COMPLEX BETWEEN E.COLI HPRT AND IMP -

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Basic information

Entry
Database: PDB / ID: 1g9s
TitleCRYSTAL STRUCTURE OF A COMPLEX BETWEEN E.COLI HPRT AND IMP
ComponentsHYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE
KeywordsTRANSFERASE / phosphoribosyltransferases / purine salvage / protein chemistry / enzymology
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 / magnesium ion binding / protein-containing complex / identical protein binding / 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
INOSINIC ACID / ANY 5'-MONOPHOSPHATE NUCLEOTIDE / Hypoxanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGuddat, L.W. / Vos, S. / Martin, J.L. / Keough, D.T. / de Jersey, J.
CitationJournal: Protein Sci. / Year: 2002
Title: Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase.
Authors: Guddat, L.W. / Vos, S. / Martin, J.L. / Keough, D.T. / de Jersey, J.
History
DepositionNov 27, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE
B: HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8784
Polymers41,3162
Non-polymers5622
Water1,72996
1
A: HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE
B: HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE
hetero molecules

A: HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE
B: HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7568
Polymers82,6324
Non-polymers1,1254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area9860 Å2
ΔGint-51 kcal/mol
Surface area26790 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)84.140, 84.140, 167.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe dimer is assembled by combination of subunit A (residues 5-181) and subunit B (residues 305-481) / the biological assembly is a tetramer generated from the dimer in the asymmetric unit and by the operation: x-y+1, -y+2, -z + 2/3

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Components

#1: Protein HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE


Mass: 20657.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: HPT / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): SPHI606
References: UniProt: P0A9M2, hypoxanthine phosphoribosyltransferase
#2: Chemical ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical ChemComp-N / ANY 5'-MONOPHOSPHATE NUCLEOTIDE / 1-DEOXY-RIBOFURANOSE-5'-PHOSPHATE


Type: RNA linking / Mass: 214.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11O7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 70.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Hepes, sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
118 mg/mlprotein1drop0.88mM in terms of subumits
20.05 MTris-HCl1drop
30.01 M1dropMgCl2
41 mMdithiothreitol1droppH7.4
50.1 MHEPES1reservoirpH7.5
60.1 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Dec 16, 1999
RadiationMonochromator: mirror and filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 17473 / Num. obs: 58776 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 38.7 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 8.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 4.5 / Num. unique all: 1248 / % possible all: 99.8
Reflection
*PLUS
Num. obs: 17473 / Num. measured all: 58776 / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 99.8 % / Rmerge(I) obs: 0.276

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: T.foetus HPRT

Resolution: 2.8→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1678 10 %Random
Rwork0.201 ---
all0.201 16939 --
obs0.201 16939 96.8 %-
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2668 0 36 96 2800
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.326 155 -
Rwork0.269 --
obs-1552 90 %
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor all: 0.201 / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.37
LS refinement shell
*PLUS
Rfactor Rfree: 0.326 / Rfactor Rwork: 0.269

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