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

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Basic information

Entry
Database: PDB / ID: 1dqn
TitleCRYSTAL STRUCTURE OF GIARDIA GUANINE PHOSPHORIBOSYLTRANSFERASE COMPLEXED WITH A TRANSITION STATE ANALOGUE
ComponentsGUANINE PHOSPHORIBOSYLTRANSFERASE
KeywordsTRANSFERASE / protein-inhibitor complex / Mg ions / pyrophosphate / transition state analogue
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-IMU / ISOPROPYL ALCOHOL / PYROPHOSPHATE 2- / 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 / pdbx_struct_conn_angle / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _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)53,9189
Polymers52,7352
Non-polymers1,1837
Water8,575476
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-43 kcal/mol
Surface area20720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.632, 71.553, 123.08
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer in the asymmetric unit

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 483 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-IMU / PHOSPHORIC ACID MONO-[5-(2-AMINO-4-OXO-4,5-DIHYDRO-3H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)-3,4-DIHYDROXY-PYRROLIDIN-2-YLMETHYL] ESTER / MODIFIED QUANOSINE-5-PHOSPHATE


Mass: 361.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16N5O7P
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 2.36 Å3/Da / Density % sol: 47.97 %
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
*PLUS
Density % sol: 47 %
Crystal grow
*PLUS
Temperature: 18 ℃
Details: cocrystallized with a 1:1:1 stoichiometry of immucillin GP, 1 mM MgCl2, and 1 mM sodium pyrophosphate
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 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: 50789 / Num. obs: 50789 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 17.7 Å2 / Rsym value: 0.036 / Net I/σ(I): 40.3
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.2 % / Num. unique all: 2481 / Rsym value: 0.082 / % possible all: 99.1
Reflection
*PLUS
Num. measured all: 195866 / Rmerge(I) obs: 0.036
Reflection shell
*PLUS
% possible obs: 99.1 % / Rmerge(I) obs: 0.082 / Mean I/σ(I) obs: 17.8

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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
Rfree0.234 5080 -random
Rwork0.204 ---
all0.211 50562 --
obs0.207 50375 98.4 %-
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3706 0 68 480 4254
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.35

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