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- PDB-3efh: Crystal structure of human phosphoribosyl pyrophosphate synthetase 1 -

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Basic information

Entry
Database: PDB / ID: 3efh
TitleCrystal structure of human phosphoribosyl pyrophosphate synthetase 1
ComponentsRibose-phosphate pyrophosphokinase 1
KeywordsTRANSFERASE / Charcot-Marie-Tooth disease / Deafness / Disease mutation / Gout / Kinase / Magnesium / Metal-binding / Nucleotide biosynthesis / Polymorphism
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 / kinase activity / nervous system development / phosphorylation / magnesium ion binding / protein homodimerization activity / ATP binding / identical protein binding / cytoplasm / cytosol
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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLi, X. / Peng, X. / Li, Y.
CitationJournal: To be Published
Title: Crystal structure of human phosphoribosyl pyrophosphate synthetase 1
Authors: Peng, X. / Li, X.
History
DepositionSep 8, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 1
B: Ribose-phosphate pyrophosphokinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4778
Polymers71,9012
Non-polymers5766
Water1,946108
1
A: Ribose-phosphate pyrophosphokinase 1
B: Ribose-phosphate pyrophosphokinase 1
hetero molecules

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

A: Ribose-phosphate pyrophosphokinase 1
B: Ribose-phosphate pyrophosphokinase 1
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_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
2
A: Ribose-phosphate pyrophosphokinase 1
hetero molecules

A: Ribose-phosphate pyrophosphokinase 1
hetero molecules

A: Ribose-phosphate pyrophosphokinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,71612
Polymers107,8513
Non-polymers8659
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area3580 Å2
ΔGint-134 kcal/mol
Surface area40380 Å2
MethodPISA
3
B: Ribose-phosphate pyrophosphokinase 1
hetero molecules

B: Ribose-phosphate pyrophosphokinase 1
hetero molecules

B: Ribose-phosphate pyrophosphokinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,71612
Polymers107,8513
Non-polymers8659
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area3630 Å2
ΔGint-137 kcal/mol
Surface area40230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.180, 169.180, 61.840
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 / Phosphoribosyl pyrophosphate synthetase I / PRS-I / PPRibP


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(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(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.: 108 / 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: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: 2.1M ammonium sulfate, 0.1M sodium acetate, 10% (v/v) glycerol, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 18, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.6→42.295 Å / Num. all: 18873 / Num. obs: 18518 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.4 % / Biso Wilson estimate: 50.4 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 8.5
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 1.8 / Num. unique all: 2623 / Rsym value: 0.345 / % possible all: 88.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HCR
Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.91 / SU B: 8.566 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23133 947 5.1 %RANDOM
Rwork0.2157 ---
all0.21649 18508 --
obs0.21649 17561 91.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.116 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20.39 Å20 Å2
2--0.79 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4592 0 30 108 4730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224680
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.081.9576352
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1195610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.55124.632190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.78115790
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8841528
X-RAY DIFFRACTIONr_chiral_restr0.0710.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023442
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.22203
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23169
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2247
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.288
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.491.53146
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.64924902
X-RAY DIFFRACTIONr_scbond_it0.82631703
X-RAY DIFFRACTIONr_scangle_it1.2434.51450
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 60 -
Rwork0.302 1265 -
obs--88.04 %

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