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- PDB-3lpn: Crystal structure of the phosphoribosylpyrophosphate (PRPP) synth... -

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Basic information

Entry
Database: PDB / ID: 3lpn
TitleCrystal structure of the phosphoribosylpyrophosphate (PRPP) synthetase from Thermoplasma volcanium in complex with an ATP analog (AMPCPP).
ComponentsRibose-phosphate pyrophosphokinase
KeywordsTRANSFERASE / Phosphoribosyltransferase / 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
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / Ribose-phosphate pyrophosphokinase
Similarity search - Component
Biological speciesThermoplasma volcanium (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 25, 2012Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 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)65,9349
Polymers64,4432
Non-polymers1,4917
Water8,953497
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-17 kcal/mol
Surface area23270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.576, 141.162, 50.039
Angle α, β, γ (deg.)90.00, 95.97, 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-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / 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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 2M Ammonium sulfate, 0.1M 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: 1.8→50 Å / Num. all: 49202 / Num. obs: 49153 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 11.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 2 / Num. unique all: 4918 / Rsym value: 0.594 / % possible all: 100

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Processing

Software
NameVersionClassification
BALBESphasing
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.4_4refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1u9y

1u9y


Resolution: 1.8→29.174 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35
RfactorNum. reflection% reflectionSelection details
Rfree0.2159 2486 5.07 %random
Rwork0.1737 ---
obs0.1758 49076 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.212 Å2 / ksol: 0.371 e/Å3
Refinement stepCycle: LAST / Resolution: 1.8→29.174 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4517 0 87 497 5101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054677
X-RAY DIFFRACTIONf_angle_d1.036336
X-RAY DIFFRACTIONf_dihedral_angle_d22.0031760
X-RAY DIFFRACTIONf_chiral_restr0.068722
X-RAY DIFFRACTIONf_plane_restr0.003797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8340.31721500.26532563X-RAY DIFFRACTION99
1.834-1.87140.24921320.23882566X-RAY DIFFRACTION100
1.8714-1.91210.27081310.22572595X-RAY DIFFRACTION100
1.9121-1.95660.27591440.22092565X-RAY DIFFRACTION100
1.9566-2.00550.24051260.20152623X-RAY DIFFRACTION100
2.0055-2.05970.22391560.19452553X-RAY DIFFRACTION100
2.0597-2.12030.2661470.18362550X-RAY DIFFRACTION100
2.1203-2.18870.21231460.18512600X-RAY DIFFRACTION100
2.1887-2.26690.25821240.17962609X-RAY DIFFRACTION100
2.2669-2.35760.23251230.16812581X-RAY DIFFRACTION100
2.3576-2.46490.21371360.16832598X-RAY DIFFRACTION100
2.4649-2.59470.23041100.17142625X-RAY DIFFRACTION100
2.5947-2.75720.23681390.18012609X-RAY DIFFRACTION100
2.7572-2.96990.2061400.18172566X-RAY DIFFRACTION100
2.9699-3.26840.21341470.17182578X-RAY DIFFRACTION100
3.2684-3.74050.20721470.15012584X-RAY DIFFRACTION100
3.7405-4.70940.16311440.1362602X-RAY DIFFRACTION100
4.7094-29.17790.18631440.16642623X-RAY DIFFRACTION100

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