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- PDB-1dqp: CRYSTAL STRUCTURE OF GIARDIA GUANINE PHOSPHORIBOSYLTRANSFERASE CO... -

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Basic information

Entry
Database: PDB / ID: 1dqp
TitleCRYSTAL STRUCTURE OF GIARDIA GUANINE PHOSPHORIBOSYLTRANSFERASE COMPLEXED WITH IMMUCILLING
ComponentsGUANINE PHOSPHORIBOSYLTRANSFERASE
KeywordsTRANSFERASE / protein-inhibitor complex / immucillinG / 9-deazaguanine
Function / homology
Function and homology information


guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / magnesium ion binding / cytosol
Similarity search - Function
: / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-IMG / ISOPROPYL ALCOHOL / Guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesGiardia intestinalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsShi, W. / Munagala, N.R. / Wang, C.C. / Li, C.M. / Tyler, P.C. / Furneaux, R.H. / Grubmeyer, C. / Schramm, V.L. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2000
Title: Crystal structures of Giardia lamblia guanine phosphoribosyltransferase at 1.75 A(,).
Authors: Shi, W. / Munagala, N.R. / Wang, C.C. / Li, C.M. / Tyler, P.C. / Furneaux, R.H. / Grubmeyer, C. / Schramm, V.L. / Almo, S.C.
History
DepositionJan 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,4176
Polymers52,7352
Non-polymers6834
Water8,737485
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-8 kcal/mol
Surface area21270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.860, 71.610, 122.369
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer in the asymmetric unit.

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Components

#1: Protein GUANINE PHOSPHORIBOSYLTRANSFERASE


Mass: 26367.279 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia intestinalis (eukaryote) / Production host: Escherichia coli (E. coli)
References: UniProt: Q24973, hypoxanthine phosphoribosyltransferase
#2: Chemical ChemComp-IMG / 1,4-DIDEOXY-1,4-IMINO-1-(S)-(9-DEAZAGUANIN-9-YL)-D-RIBITOL / IMMUCILLIN-G


Mass: 281.268 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N5O4
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details9-deazaguanine is the only part of immucillinG ligand that could be seen in the density. Because ...9-deazaguanine is the only part of immucillinG ligand that could be seen in the density. Because immucillinG lacks a 5'-phosphate group, the sugar part of the ligand is not well ordered in this structure.

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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: 2.36 Å3/Da / Density % sol: 47.92 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% polyethylene glycol 4000, 5% isopropanol, 100 mM Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
220 %PEG40001reservoir
35 %2-propanol1reservoir
4100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 22, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. all: 50590 / Num. obs: 50590 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 17 Å2 / Rsym value: 0.039 / Net I/σ(I): 40.8
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.6 % / Num. unique all: 2485 / Rsym value: 0.075 / % possible all: 98.7
Reflection
*PLUS
Num. measured all: 210690 / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 98.7 % / Rmerge(I) obs: 0.075

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.75→20 Å / σ(F): 2 / σ(I): 1.4 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.232 5053 -random
Rwork0.204 ---
all0.21 50347 --
obs0.207 50175 98.1 %-
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3709 0 22 493 4224
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 45122
Solvent computation
*PLUS
Displacement parameters
*PLUS

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