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- PDB-1g2q: CRYSTAL STRUCTURE OF ADENINE PHOSPHORIBOSYLTRANSFERASE -

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Basic information

Entry
Database: PDB / ID: 1g2q
TitleCRYSTAL STRUCTURE OF ADENINE PHOSPHORIBOSYLTRANSFERASE
ComponentsADENINE PHOSPHORIBOSYLTRANSFERASE 1
KeywordsTRANSFERASE / dimer / single domain / catalytic loop
Function / homology
Function and homology information


Purine salvage / adenine binding / adenine salvage / adenine phosphoribosyltransferase activity / adenine phosphoribosyltransferase / AMP salvage / purine ribonucleoside salvage / AMP binding / Neutrophil degranulation / metal ion binding ...Purine salvage / adenine binding / adenine salvage / adenine phosphoribosyltransferase activity / adenine phosphoribosyltransferase / AMP salvage / purine ribonucleoside salvage / AMP binding / Neutrophil degranulation / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Adenine 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
Adenine phosphoribosyltransferase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsShi, W. / Tanaka, K.S.E. / Almo, S.C. / Schramm, V.L.
CitationJournal: Biochemistry / Year: 2001
Title: Structural analysis of adenine phosphoribosyltransferase from Saccharomyces cerevisiae.
Authors: Shi, W. / Tanaka, K.S. / Crother, T.R. / Taylor, M.W. / Almo, S.C. / Schramm, V.L.
History
DepositionOct 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADENINE PHOSPHORIBOSYLTRANSFERASE 1
B: ADENINE PHOSPHORIBOSYLTRANSFERASE 1


Theoretical massNumber of molelcules
Total (without water)41,2342
Polymers41,2342
Non-polymers00
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-17 kcal/mol
Surface area15740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.661, 45.767, 53.883
Angle α, β, γ (deg.)95.694, 108.403, 109.585
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a dimer in the asymmetric unit.

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Components

#1: Protein ADENINE PHOSPHORIBOSYLTRANSFERASE 1 /


Mass: 20616.814 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PQE / Production host: Escherichia coli (E. coli)
References: UniProt: P49435, adenine phosphoribosyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.18 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 5000 MME, sodium acetate, citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMsodium citrate1reservoirpH5.5
20.2 Msodium acetate1reservoir
320 %PEG5000 MME1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 14, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 54848 / Num. obs: 54848 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 16.1 Å2 / Rsym value: 0.024 / Net I/σ(I): 34.4
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 5137 / Rsym value: 0.176 / % possible all: 89.9
Reflection
*PLUS
Num. measured all: 132505 / Rmerge(I) obs: 0.024
Reflection shell
*PLUS
% possible obs: 89.9 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 3.9

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1G2P

1g2p


Resolution: 1.5→20 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1.4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 5084 10.1 %random
Rwork0.199 ---
obs0.202 50300 88.5 %-
all-53229 --
Solvent computationSolvent model: Flat Model / Bsol: 53.7292 Å2 / ksol: 0.414732 e/Å3
Displacement parametersBiso mean: 19.3 Å2
Baniso -1Baniso -2Baniso -3
1-4.46 Å23.03 Å22.08 Å2
2---3.55 Å21.81 Å2
3----0.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2772 0 0 305 3077
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it0.651.5
X-RAY DIFFRACTIONc_mcangle_it1.12
X-RAY DIFFRACTIONc_scbond_it1.082
X-RAY DIFFRACTIONc_scangle_it1.652.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.247 719 10.3 %
Rwork0.231 6264 -
obs-4264 74 %
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 10.1 % / Rfactor all: 0.202 / Rfactor obs: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.345
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89
X-RAY DIFFRACTIONc_mcbond_it0.651.5
X-RAY DIFFRACTIONc_scbond_it1.082
X-RAY DIFFRACTIONc_mcangle_it1.12
X-RAY DIFFRACTIONc_scangle_it1.652.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.247 / % reflection Rfree: 10.3 % / Rfactor Rwork: 0.231

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