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- PDB-4lzn: Crystal structure of human PRS1 D65N mutant -

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Basic information

Entry
Database: PDB / ID: 4lzn
TitleCrystal structure of human PRS1 D65N mutant
ComponentsRibose-phosphate pyrophosphokinase 1
KeywordsTRANSFERASE / PRS1 / PRPP synthesis enzyme / ATP R5P
Function / homology
Function and homology information


5-Phosphoribose 1-diphosphate biosynthesis / hypoxanthine biosynthetic process / ribose phosphate diphosphokinase complex / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / ribonucleoside monophosphate biosynthetic process / 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 / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / ribonucleoside monophosphate biosynthetic process / urate biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / pyrimidine nucleotide biosynthetic process / purine nucleotide biosynthetic process / purine nucleobase metabolic process / nervous system development / kinase activity / phosphorylation / 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 / N-terminal domain of ribose phosphate pyrophosphokinase / Phosphoribosyl synthetase-associated domain / 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 / N-terminal domain of ribose phosphate pyrophosphokinase / Phosphoribosyl synthetase-associated domain / 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: 2.14 Å
AuthorsChen, P. / Teng, M. / Li, X.
CitationJournal: Plos One / Year: 2015
Title: Crystal and EM Structures of Human Phosphoribosyl Pyrophosphate Synthase I (PRS1) Provide Novel Insights into the Disease-Associated Mutations
Authors: Chen, P. / Liu, Z. / Wang, X. / Peng, J. / Sun, Q. / Li, J. / Wang, M. / Niu, L. / Zhang, Z. / Cai, G. / Teng, M. / Li, X.
History
DepositionJul 31, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Nov 8, 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
B: Ribose-phosphate pyrophosphokinase 1
A: Ribose-phosphate pyrophosphokinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4758
Polymers71,8992
Non-polymers5766
Water1,24369
1
B: Ribose-phosphate pyrophosphokinase 1
A: Ribose-phosphate pyrophosphokinase 1
hetero molecules

B: Ribose-phosphate pyrophosphokinase 1
A: Ribose-phosphate pyrophosphokinase 1
hetero molecules

B: Ribose-phosphate pyrophosphokinase 1
A: Ribose-phosphate pyrophosphokinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,42524
Polymers215,6966
Non-polymers1,72918
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area28930 Å2
ΔGint-429 kcal/mol
Surface area59030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.776, 170.776, 61.698
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 1 / PPRibP / Phosphoribosyl pyrophosphate synthase I / PRS-I


Mass: 35949.391 Da / Num. of mol.: 2 / Mutation: D65N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRPS1 / Production host: Escherichia coli (E. coli)
References: UniProt: P60891, ribose-phosphate diphosphokinase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.41 Å3/Da / Density % sol: 48.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 4.1 / Details: pH 4.1, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→49.3 Å / Num. obs: 35171

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F8E

4f8e


Resolution: 2.14→49.3 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.893 / SU B: 5.857 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.287 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26319 1759 5 %RANDOM
Rwork0.2242 ---
obs0.22621 33412 95.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.204 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20.7 Å20 Å2
2--1.4 Å20 Å2
3----2.1 Å2
Refinement stepCycle: LAST / Resolution: 2.14→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4673 0 30 69 4772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224770
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0661.9596453
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3415608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52124.523199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.54215855
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.631530
X-RAY DIFFRACTIONr_chiral_restr0.0730.2763
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213478
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3431.53039
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.65924916
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.11531731
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.464.51537
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.142→2.197 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 87 -
Rwork0.27 1748 -
obs--68.22 %

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