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- PDB-2h06: Crystal structure of human phosphoribosyl pyrophosphate synthetase 1 -

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Basic information

Entry
Database: PDB / ID: 2h06
TitleCrystal structure of human phosphoribosyl pyrophosphate synthetase 1
ComponentsRibose-phosphate pyrophosphokinase I
KeywordsTRANSFERASE / PRS1 / prpp synthetase 1 / phosphoribosyl pyrophosphate synthetase 1
Function / homology
Function and homology information


5-Phosphoribose 1-diphosphate biosynthesis / hypoxanthine biosynthetic process / ribose phosphate diphosphokinase complex / ribonucleoside monophosphate biosynthetic process / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / urate biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / pyrimidine nucleotide biosynthetic process / purine nucleotide biosynthetic process ...5-Phosphoribose 1-diphosphate biosynthesis / hypoxanthine biosynthetic process / ribose phosphate diphosphokinase complex / ribonucleoside monophosphate biosynthetic process / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / urate biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / pyrimidine nucleotide biosynthetic process / purine nucleotide biosynthetic process / purine nucleobase metabolic process / kinase activity / nervous system development / magnesium ion binding / protein homodimerization activity / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Phosphoribosyl pyrophosphate synthetase, conserved site / Phosphoribosyl pyrophosphate synthase signature. / Ribose-phosphate pyrophosphokinase, bacterial-type / Phosphoribosyl synthetase-associated domain / 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 / Phosphoribosyltransferase-like ...Phosphoribosyl pyrophosphate synthetase, conserved site / Phosphoribosyl pyrophosphate synthase signature. / Ribose-phosphate pyrophosphokinase, bacterial-type / Phosphoribosyl synthetase-associated domain / 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 / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribose-phosphate pyrophosphokinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLi, S. / Peng, B. / Ding, J.
CitationJournal: Biochem.J. / Year: 2007
Title: Crystal structure of human phosphoribosylpyrophosphate synthetase 1 reveals a novel allosteric site
Authors: Li, S. / Lu, Y. / Peng, B. / Ding, J.
History
DepositionMay 14, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 I
B: Ribose-phosphate pyrophosphokinase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4778
Polymers71,9012
Non-polymers5766
Water3,297183
1
A: Ribose-phosphate pyrophosphokinase I
B: Ribose-phosphate pyrophosphokinase I
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)217,43124
Polymers215,7026
Non-polymers1,72918
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area28920 Å2
ΔGint-443 kcal/mol
Surface area59120 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)169.683, 169.683, 61.598
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Ribose-phosphate pyrophosphokinase I / Phosphoribosyl pyrophosphate synthetase I / PRS-I / PPRibP / PRPP synthetase 1


Mass: 35950.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRPS1 / Plasmid: pET-22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3)
References: UniProt: P60891, ribose-phosphate diphosphokinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.15
Details: 0.1M citric acid, 1.3M ammonium sulfate, 0.02M sodium dihydrogen phosphate, 0.4M sodium chloride, pH 4.15, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 33560 / Num. obs: 33517 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 16.8
Reflection shellResolution: 2.2→2.28 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DKR

1dkr


Resolution: 2.2→48.98 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2718982.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1676 5 %RANDOM
Rwork0.212 ---
obs0.212 33517 99.7 %-
all-33560 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.0654 Å2 / ksol: 0.386452 e/Å3
Displacement parametersBiso mean: 43.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.86 Å24.97 Å20 Å2
2--3.86 Å20 Å2
3----7.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.2→48.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4691 0 30 183 4904
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.342 303 5.4 %
Rwork0.287 5266 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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