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- PDB-2hcr: crystal structure of human phosphoribosyl pyrophosphate synthetas... -

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Basic information

Entry
Database: PDB / ID: 2hcr
Titlecrystal structure of human phosphoribosyl pyrophosphate synthetase 1 in complex with AMP(ATP), cadmium and sulfate ion
ComponentsRibose-phosphate pyrophosphokinase I
KeywordsTRANSFERASE / PRS1 / prpp synthetase 1 / phosphoribosyl pyrophosphate 1
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
ADENOSINE MONOPHOSPHATE / : / Ribose-phosphate pyrophosphokinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / 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
DepositionJun 18, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _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)73,39612
Polymers71,9012
Non-polymers1,49610
Water2,594144
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)220,18936
Polymers215,7026
Non-polymers4,48730
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area34550 Å2
ΔGint-491 kcal/mol
Surface area58020 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)170.236, 170.236, 61.820
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.4 Å3/Da / Density % sol: 48.69 %
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, 0.01M ATP, 0.01M cadmium chloride, pH 4.15, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 2, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. all: 33914 / Num. obs: 32945 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.59 % / Rmerge(I) obs: 0.074 / Χ2: 1.2 / Net I/σ(I): 7.9 / Scaling rejects: 9751
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.2-2.285.670.3592.11890832891.0196.8
2.28-2.375.660.3132.41911433131.0697
2.37-2.485.620.2572.81903732961.197.4
2.48-2.615.640.2233.21913933051.1698
2.61-2.775.640.1794.11932233251.2298.1
2.77-2.985.650.1355.31940033061.397.6
2.98-3.285.620.0937.61956633161.397.5
3.28-3.765.560.059121963332891.3497.1
3.76-4.735.480.03818.41978933021.397.3
4.73-24.665.330.0322.41989732041.2594.7

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Phasing

Phasing MRCor.coef. Fo:Fc: 0.773 / Packing: 0.565
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Translation4 Å15 Ågeneral96.8 1

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Processing

Software
NameVersionClassificationNB
d*TREK7.1SSIdata scaling
CNSrefinement
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H06

2h06


Resolution: 2.2→25 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.921 / SU B: 13.692 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1672 5.1 %RANDOM
Rwork0.205 ---
all0.208 33914 --
obs0.205 32941 97.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.369 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.11 Å20 Å2
2--0.21 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4691 0 78 144 4913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224833
X-RAY DIFFRACTIONr_angle_refined_deg1.1631.9736547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3935609
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44524.45200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.76815858
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3641531
X-RAY DIFFRACTIONr_chiral_restr0.0760.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023517
X-RAY DIFFRACTIONr_nbd_refined0.1940.22253
X-RAY DIFFRACTIONr_nbtor_refined0.2940.23307
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2250
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.2119
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.214
X-RAY DIFFRACTIONr_mcbond_it1.1171.53137
X-RAY DIFFRACTIONr_mcangle_it1.62824928
X-RAY DIFFRACTIONr_scbond_it2.68131890
X-RAY DIFFRACTIONr_scangle_it2.8074.51619
X-RAY DIFFRACTIONr_rigid_bond_restr2.95635027
X-RAY DIFFRACTIONr_sphericity_free2.8633146
X-RAY DIFFRACTIONr_sphericity_bonded1.38434769
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 142 -
Rwork0.251 2297 -
obs-2439 96.9 %

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