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- PDB-3lrt: Crystal structure of the phosphoribosyl pyrophosphate (PRPP) synt... -

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Basic information

Entry
Database: PDB / ID: 3lrt
TitleCrystal structure of the phosphoribosyl pyrophosphate (PRPP) synthetase from Thermoplasma volcanium in complex with ADP.
ComponentsRibose-phosphate pyrophosphokinase
KeywordsTRANSFERASE / Phosphoribosyl transferase / ATP analog binding / ATP-binding / Kinase / Metal-binding / Nucleotide biosynthesis / Nucleotide-binding
Function / homology
Function and homology information


ribose phosphate diphosphokinase complex / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / 5-phosphoribose 1-diphosphate biosynthetic process / purine nucleotide biosynthetic process / kinase activity / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Ribose-phosphate pyrophosphokinase, archaea / N-terminal domain of ribose phosphate pyrophosphokinase / Ribose-phosphate pyrophosphokinase / Ribose-phosphate pyrophosphokinase, N-terminal domain / N-terminal domain of ribose phosphate pyrophosphokinase / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold ...Ribose-phosphate pyrophosphokinase, archaea / N-terminal domain of ribose phosphate pyrophosphokinase / Ribose-phosphate pyrophosphokinase / Ribose-phosphate pyrophosphokinase, N-terminal domain / N-terminal domain of ribose phosphate pyrophosphokinase / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Ribose-phosphate pyrophosphokinase
Similarity search - Component
Biological speciesThermoplasma volcanium (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.534 Å
AuthorsCherney, M.M. / Cherney, L.T. / Garen, C.R. / James, M.N.G.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The structures of Thermoplasma volcanium phosphoribosyl pyrophosphate synthetase bound to ribose-5-phosphate and ATP analogs.
Authors: Cherney, M.M. / Cherney, L.T. / Garen, C.R. / James, M.N.
History
DepositionFeb 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 25, 2012Group: Database references
Revision 1.3Sep 6, 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

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Assembly

Deposited unit
A: Ribose-phosphate pyrophosphokinase
B: Ribose-phosphate pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6828
Polymers64,4432
Non-polymers1,2396
Water7,981443
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-17 kcal/mol
Surface area23320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.572, 141.596, 50.118
Angle α, β, γ (deg.)90.00, 96.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribose-phosphate pyrophosphokinase / RPPK / Phosphoribosyl pyrophosphate synthetase / P-Rib-PP synthetase / PRPP synthetase


Mass: 32221.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma volcanium (archaea) / Strain: ATCC51530 / Gene: prs, TV0197, TVG0201915, TVN0197 / Plasmid: pvp16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) plyss
References: UniProt: Q97CA5, ribose-phosphate diphosphokinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.11 Å3/Da / Density % sol: 41.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 2M ammonium sulfate, 0.1 M sodium citrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. all: 79457 / Num. obs: 71194 / % possible obs: 89.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 12.4
Reflection shellResolution: 1.53→1.58 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 1.6 / Num. unique all: 4586 / Rsym value: 0.418 / % possible all: 58.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LPN

3lpn


Resolution: 1.534→24.62 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 3366 5.09 %random
Rwork0.1863 ---
obs0.1881 66070 83.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.061 Å2 / ksol: 0.4 e/Å3
Refinement stepCycle: LAST / Resolution: 1.534→24.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4517 0 74 443 5034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064731
X-RAY DIFFRACTIONf_angle_d1.0586413
X-RAY DIFFRACTIONf_dihedral_angle_d17.8711783
X-RAY DIFFRACTIONf_chiral_restr0.078726
X-RAY DIFFRACTIONf_plane_restr0.004815
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.534-1.5560.3258550.2261341X-RAY DIFFRACTION43
1.556-1.57930.3044840.22821612X-RAY DIFFRACTION51
1.5793-1.60390.25751010.21441852X-RAY DIFFRACTION59
1.6039-1.63020.28931000.21082023X-RAY DIFFRACTION64
1.6302-1.65830.27451180.21292161X-RAY DIFFRACTION69
1.6583-1.68850.25511150.21042261X-RAY DIFFRACTION72
1.6885-1.72090.23281360.21472335X-RAY DIFFRACTION75
1.7209-1.75610.22611280.20712356X-RAY DIFFRACTION75
1.7561-1.79420.21931640.2012479X-RAY DIFFRACTION80
1.7942-1.8360.221190.19192600X-RAY DIFFRACTION82
1.836-1.88190.20751450.19432682X-RAY DIFFRACTION86
1.8819-1.93270.23531370.19542637X-RAY DIFFRACTION83
1.9327-1.98960.21811590.18892847X-RAY DIFFRACTION91
1.9896-2.05380.2261690.17892939X-RAY DIFFRACTION94
2.0538-2.12710.25921550.17393030X-RAY DIFFRACTION96
2.1271-2.21220.18781790.16933019X-RAY DIFFRACTION97
2.2122-2.31280.21571550.17782959X-RAY DIFFRACTION94
2.3128-2.43470.18431560.17743087X-RAY DIFFRACTION98
2.4347-2.58710.25021330.19143128X-RAY DIFFRACTION98
2.5871-2.78660.25491580.1923120X-RAY DIFFRACTION99
2.7866-3.06650.21751900.18563059X-RAY DIFFRACTION99
3.0665-3.50920.19891860.17053141X-RAY DIFFRACTION99
3.5092-4.4170.18651670.15563052X-RAY DIFFRACTION97
4.417-24.62320.22551570.19872984X-RAY DIFFRACTION93

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