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

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Basic information

Entry
Database: PDB / ID: 3nag
TitleCrystal structure of the phosphoribosylpyrophosphate (PRPP) synthetase from Thermoplasma Volcanium in complex with ADP
ComponentsRibose-phosphate pyrophosphokinase
KeywordsTRANSFERASE / phosphoribosyl transferase / ADP binding
Function / homology
Function and homology information


ribose phosphate diphosphokinase complex / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / ribonucleoside monophosphate biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / purine nucleotide biosynthetic process / kinase activity / phosphorylation / 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 GSS1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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
DepositionJun 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 25, 2012Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,47110
Polymers64,4432
Non-polymers1,0288
Water8,215456
1
A: Ribose-phosphate pyrophosphokinase
B: Ribose-phosphate pyrophosphokinase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)130,94220
Polymers128,8864
Non-polymers2,05616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-16 kcal/mol
Surface area23440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.561, 141.563, 49.620
Angle α, β, γ (deg.)90.00, 95.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 32221.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma volcanium GSS1 (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.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / 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: 2.09 Å3/Da / Density % sol: 41.16 %
Crystal growTemperature: 293 K / 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
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: 1.748→50 Å / Num. obs: 50011 / % possible obs: 93.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 14
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.835 / Mean I/σ(I) obs: 1.4 / Rsym value: 0.835 / % possible all: 80.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6.1_357)model building
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.6.1_357phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→31.92 Å / SU ML: 0.19 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 2537 5.08 %
Rwork0.176 --
obs0.178 49953 93.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.1 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.7561 Å2-0 Å22.6853 Å2
2---6.482 Å20 Å2
3----2.2741 Å2
Refinement stepCycle: LAST / Resolution: 1.75→31.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4517 0 58 456 5031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074649
X-RAY DIFFRACTIONf_angle_d1.0656293
X-RAY DIFFRACTIONf_dihedral_angle_d13.1441737
X-RAY DIFFRACTIONf_chiral_restr0.074714
X-RAY DIFFRACTIONf_plane_restr0.003796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.748-1.78120.35271120.28172001X-RAY DIFFRACTION72
1.7812-1.81760.27181140.25152463X-RAY DIFFRACTION88
1.8176-1.85710.27441230.23572518X-RAY DIFFRACTION88
1.8571-1.90030.28861290.22792511X-RAY DIFFRACTION90
1.9003-1.94780.27841330.21482569X-RAY DIFFRACTION91
1.9478-2.00040.29671210.19762610X-RAY DIFFRACTION92
2.0004-2.05930.24251470.18612646X-RAY DIFFRACTION94
2.0593-2.12570.22291700.18432609X-RAY DIFFRACTION94
2.1257-2.20170.2161490.17812663X-RAY DIFFRACTION96
2.2017-2.28980.26621470.17542697X-RAY DIFFRACTION96
2.2898-2.3940.21031510.16922698X-RAY DIFFRACTION96
2.394-2.52020.1991490.16822726X-RAY DIFFRACTION97
2.5202-2.6780.2411460.17092738X-RAY DIFFRACTION98
2.678-2.88460.21441600.17682739X-RAY DIFFRACTION98
2.8846-3.17470.23361500.17372771X-RAY DIFFRACTION98
3.1747-3.63350.17821440.16182796X-RAY DIFFRACTION99
3.6335-4.57570.17231450.13932824X-RAY DIFFRACTION99
4.5757-31.92130.19721470.17482837X-RAY DIFFRACTION99

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