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- PDB-4twb: Sulfolobus solfataricus ribose-phosphate pyrophosphokinase -

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Basic information

Entry
Database: PDB / ID: 4twb
TitleSulfolobus solfataricus ribose-phosphate pyrophosphokinase
ComponentsRibose-phosphate pyrophosphokinase
KeywordsTRANSFERASE
Function / homology
Function and homology information


ribose phosphate diphosphokinase complex / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / ribonucleoside monophosphate biosynthetic process / nucleotide biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / nucleoside metabolic process / purine nucleotide biosynthetic process / kinase activity / magnesium ion binding ...ribose phosphate diphosphokinase complex / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / ribonucleoside monophosphate biosynthetic process / nucleotide biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / nucleoside metabolic process / purine nucleotide biosynthetic process / kinase activity / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Ribose-phosphate pyrophosphokinase, archaea / 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-phosphate pyrophosphokinase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.802 Å
AuthorsKadziola, A.
CitationJournal: Extremophiles / Year: 2015
Title: Structure of dimeric, recombinant Sulfolobus solfataricus phosphoribosyl diphosphate synthase: a bent dimer defining the adenine specificity of the substrate ATP.
Authors: Andersen, R.W. / Leggio, L.L. / Hove-Jensen, B. / Kadziola, A.
History
DepositionJun 30, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Mar 4, 2015Group: Database references
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Feb 14, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 1.5Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
E: Ribose-phosphate pyrophosphokinase
F: Ribose-phosphate pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,99918
Polymers193,3396
Non-polymers2,66012
Water43224
1
A: Ribose-phosphate pyrophosphokinase
B: Ribose-phosphate pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3336
Polymers64,4462
Non-polymers8874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-49 kcal/mol
Surface area22740 Å2
MethodPISA
2
C: Ribose-phosphate pyrophosphokinase
D: Ribose-phosphate pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3336
Polymers64,4462
Non-polymers8874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-29 kcal/mol
Surface area22710 Å2
MethodPISA
3
E: Ribose-phosphate pyrophosphokinase
F: Ribose-phosphate pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3336
Polymers64,4462
Non-polymers8874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-28 kcal/mol
Surface area22740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.217, 92.846, 138.338
Angle α, β, γ (deg.)90.00, 90.91, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 1:190 or resseq 204:291 or resseq 301:302 or resseq 402:405 )
211chain B and (resseq 1:190 or resseq 204:291 or resseq 301:302 or resseq 402:405 )
112chain A and (resseq 1:190 or resseq 204:291 or resseq 301:302 or resseq 402:405 )
212chain C and (resseq 1:190 or resseq 204:291 or resseq 301:302 or resseq 402:405 )
113chain A and (resseq 1:190 or resseq 204:291 or resseq 301:302 or resseq 402:405 )
213chain D and (resseq 1:190 or resseq 204:291 or resseq 301:302 or resseq 402:405 )
114chain A and (resseq 1:190 or resseq 204:291 or resseq 301:302 or resseq 402:405 )
214chain E and (resseq 1:190 or resseq 204:291 or resseq 301:302 or resseq 402:405 )
115chain A and (resseq 1:190 or resseq 204:291 or resseq 301:302 or resseq 402:405 )
215chain F and (resseq 1:190 or resseq 204:291 or resseq 301:302 or resseq 402:405 )

NCS ensembles :
ID
1
2
3
4
5

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Components

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


Mass: 32223.221 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Production host: Escherichia coli (E. coli)
References: UniProt: Q97Z86, ribose-phosphate diphosphokinase
#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.83 % / Description: 350*100*100 um3
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5
Details: Protein: 12.7 mg/mL 50 mM Tris/HCl pH 7.6 10 mM AMP 10 mM ribose 5-phosphate Buffer: 0.2 M diammonium citrate pH 5.0 Precipitant: 14 % PEG10000

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03908 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03908 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 48432 / Num. obs: 48432 / % possible obs: 97.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 14
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.4 / % possible all: 98.1

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX(phenix.refine)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U9Y

1u9y


Resolution: 2.802→19.984 Å / SU ML: 1.1 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2647 2406 4.97 %5 % random selection
Rwork0.2346 ---
obs0.2361 48382 97.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.012 Å2 / ksol: 0.308 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.7424 Å20 Å2-16.2902 Å2
2---0.312 Å20 Å2
3----6.4304 Å2
Refinement stepCycle: LAST / Resolution: 2.802→19.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13002 0 168 24 13194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913350
X-RAY DIFFRACTIONf_angle_d1.30618102
X-RAY DIFFRACTIONf_dihedral_angle_d18.7555022
X-RAY DIFFRACTIONf_chiral_restr0.0822208
X-RAY DIFFRACTIONf_plane_restr0.0042256
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2199X-RAY DIFFRACTIONPOSITIONAL
12B2199X-RAY DIFFRACTIONPOSITIONAL0.05
21A2199X-RAY DIFFRACTIONPOSITIONAL
22C2199X-RAY DIFFRACTIONPOSITIONAL0.061
31A2199X-RAY DIFFRACTIONPOSITIONAL
32D2199X-RAY DIFFRACTIONPOSITIONAL0.067
41A2199X-RAY DIFFRACTIONPOSITIONAL
42E2199X-RAY DIFFRACTIONPOSITIONAL0.058
51A2199X-RAY DIFFRACTIONPOSITIONAL
52F2199X-RAY DIFFRACTIONPOSITIONAL0.056
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8015-2.85860.38561100.31122587X-RAY DIFFRACTION47
2.8586-2.92050.37231570.28472718X-RAY DIFFRACTION50
2.9205-2.98830.28981380.28242746X-RAY DIFFRACTION50
2.9883-3.06270.36341480.28072689X-RAY DIFFRACTION50
3.0627-3.14520.34461560.26972719X-RAY DIFFRACTION50
3.1452-3.23740.26391600.26122704X-RAY DIFFRACTION50
3.2374-3.34140.35011490.26042739X-RAY DIFFRACTION50
3.3414-3.46030.29731390.26382722X-RAY DIFFRACTION50
3.4603-3.59810.38181170.31042545X-RAY DIFFRACTION46
3.5981-3.76080.39191220.33532599X-RAY DIFFRACTION47
3.7608-3.95760.26741340.23952701X-RAY DIFFRACTION49
3.9576-4.20340.2491470.19762671X-RAY DIFFRACTION49
4.2034-4.52450.19431400.17522758X-RAY DIFFRACTION50
4.5245-4.97340.18871380.16422744X-RAY DIFFRACTION50
4.9734-5.67860.16751510.16812766X-RAY DIFFRACTION51
5.6786-7.10070.20611490.19362784X-RAY DIFFRACTION51
7.1007-19.98490.18721510.17332784X-RAY DIFFRACTION51

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