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- PDB-1g2p: CRYSTAL STRUCTURE OF ADENINE PHOSPHORIBOSYLTRANSFERASE -

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Basic information

Entry
Database: PDB / ID: 1g2p
TitleCRYSTAL STRUCTURE OF ADENINE PHOSPHORIBOSYLTRANSFERASE
ComponentsADENINE PHOSPHORIBOSYLTRANSFERASE 1
KeywordsTRANSFERASE / dimer / catalytic loop
Function / homology
Function and homology information


Purine salvage / adenine binding / adenine salvage / adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / AMP salvage / purine ribonucleoside salvage / AMP binding / Neutrophil degranulation / metal ion binding ...Purine salvage / adenine binding / adenine salvage / adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / 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: 1.75 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: Derived calculations / Version format compliance
Revision 1.3Aug 9, 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 / 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: ADENINE PHOSPHORIBOSYLTRANSFERASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8093
Polymers20,6171
Non-polymers1922
Water1,946108
1
A: ADENINE PHOSPHORIBOSYLTRANSFERASE 1
hetero molecules

A: ADENINE PHOSPHORIBOSYLTRANSFERASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6186
Polymers41,2342
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_755-x+2,-y+1/2,z1
Buried area4020 Å2
ΔGint-83 kcal/mol
Surface area14100 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)49.426, 96.670, 112.075
Angle α, β, γ (deg.)90, 90, 90
Int Tables number24
Space group name H-MI212121
DetailsThe second part of the biological assemble is generated by the two fold screw axis, -x, -y+1/2, z

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Components

#1: Protein ADENINE PHOSPHORIBOSYLTRANSFERASE 1


Mass: 20616.814 Da / Num. of mol.: 1
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 3.19 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: lithium sulfate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
113-15 mg/mlprotein1drop
2100 mMHEPES1reservoirpH7.5
31.5 Mlithium sulfate1reservoir

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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: Jul 11, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. all: 26348 / Num. obs: 26348 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 15.9 Å2 / Rsym value: 0.041 / Net I/σ(I): 29.6
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 1134 / Rsym value: 0.24 / % possible all: 82.8
Reflection
*PLUS
Num. measured all: 103449 / Rmerge(I) obs: 0.041
Reflection shell
*PLUS
% possible obs: 82.8 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1QB8

1qb8


Resolution: 1.75→20 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1.4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2498 9.8 %random
Rwork0.208 ---
obs0.21 25435 92.4 %-
all-26354 --
Solvent computationSolvent model: Flat model / Bsol: 49.4464 Å2 / ksol: 0.370397 e/Å3
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å20 Å20 Å2
2---4.41 Å20 Å2
3---5.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1317 0 10 108 1435
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_mcbond_it1.771.5
X-RAY DIFFRACTIONc_mcangle_it2.612
X-RAY DIFFRACTIONc_scbond_it2.942
X-RAY DIFFRACTIONc_scangle_it4.172.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.329 349 9.8 %
Rwork0.3 3211 -
obs-3211 79 %
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 9.8 % / Rfactor all: 0.21 / Rfactor obs: 0.208 / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.433
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.96
X-RAY DIFFRACTIONc_mcbond_it1.771.5
X-RAY DIFFRACTIONc_scbond_it2.942
X-RAY DIFFRACTIONc_mcangle_it2.612
X-RAY DIFFRACTIONc_scangle_it4.172.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.329 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.3

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