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- PDB-1u9z: Crystal Structure of Phosphoribosyl Diphosphate Synthase Complexe... -

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Basic information

Entry
Database: PDB / ID: 1u9z
TitleCrystal Structure of Phosphoribosyl Diphosphate Synthase Complexed with AMP and Ribose 5-Phosphate
ComponentsRibose-phosphate pyrophosphokinase
KeywordsTRANSFERASE / PRPP synthase / ribose 5-phosphate / adenosine 5'-monophosphate
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 MONOPHOSPHATE / RIBOSE-5-PHOSPHATE / Ribose-phosphate pyrophosphokinase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsKadziola, A. / Johansson, E. / Jepsen, C.H. / McGuire, J. / Larsen, S. / Hove-Jensen, B.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Novel class III phosphoribosyl diphosphate synthase: structure and properties of the tetrameric, phosphate-activated, non-allosterically inhibited enzyme from Methanocaldococcus jannaschii
Authors: Kadziola, A. / Jepsen, C.H. / Johansson, E. / McGuire, J. / Larsen, S. / Hove-Jensen, B.
History
DepositionAug 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 23, 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: Ribose-phosphate pyrophosphokinase
B: Ribose-phosphate pyrophosphokinase
C: Ribose-phosphate pyrophosphokinase
D: Ribose-phosphate pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,04212
Polymers125,7334
Non-polymers2,3098
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16540 Å2
ΔGint-38 kcal/mol
Surface area37710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.260, 138.250, 138.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein
Ribose-phosphate pyrophosphokinase / E.C.2.7.6.1 / Phosphoribosyl Diphosphate Synthase / RPPK / Phosphoribosyl pyrophosphate synthetase / P-Rib-PP ...Phosphoribosyl Diphosphate Synthase / RPPK / Phosphoribosyl pyrophosphate synthetase / P-Rib-PP synthetase / PRPP synthetase


Mass: 31433.258 Da / Num. of mol.: 4 / Fragment: Phosphoribosyl Diphosphate Synthase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: prs / Production host: Escherichia coli (E. coli)
References: UniProt: Q58761, ribose-phosphate diphosphokinase
#2: Sugar
ChemComp-R5P / RIBOSE-5-PHOSPHATE


Type: saccharide / Mass: 230.110 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H11O8P
#3: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.74 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.087 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 11, 2003
RadiationMonochromator: single Si(111) monochromator crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.087 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. all: 34117 / Num. obs: 34117 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.105 / Net I/σ(I): 10.5
Reflection shellResolution: 2.8→2.87 Å / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 1.9 / % possible all: 98.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: Apo structure of Methanocaldococcus jannaschii PRPP synthase PDBID 1u9y

1u9y


Resolution: 2.8→25 Å
Isotropic thermal model: neighbour restrained B-factor optimization
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1676 5 %random
Rwork0.238 ---
all0.24 34117 --
obs0.24 34117 99.5 %-
Displacement parametersBiso mean: 44.2 Å2
Refinement stepCycle: LAST / Resolution: 2.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8524 0 148 206 8878
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008659
X-RAY DIFFRACTIONc_angle_deg1.29645

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