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- PDB-1ibs: PHOSPHORIBOSYLDIPHOSPHATE SYNTHETASE IN COMPLEX WITH CADMIUM IONS -

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Basic information

Entry
Database: PDB / ID: 1ibs
TitlePHOSPHORIBOSYLDIPHOSPHATE SYNTHETASE IN COMPLEX WITH CADMIUM IONS
ComponentsRIBOSE-PHOSPHATE PYROPHOSPHOKINASE
KeywordsTRANSFERASE / Open alpha beta structure / Domain duplication / Phosphoribosyltransferase type I fold
Function / homology
Function and homology information


ribose phosphate diphosphokinase complex / ribonucleoside monophosphate biosynthetic process / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / 5-phosphoribose 1-diphosphate biosynthetic process / purine nucleotide biosynthetic process / kinase activity / magnesium ion binding / ATP binding / 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
METHYL PHOSPHONIC ACID ADENOSINE ESTER / : / Ribose-phosphate pyrophosphokinase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsEriksen, T.A. / Kadziola, A. / Larsen, S.
CitationJournal: Protein Sci. / Year: 2002
Title: Binding of cations in Bacillus subtilis phosphoribosyldiphosphate synthetase and their role in catalysis.
Authors: Eriksen, T.A. / Kadziola, A. / Larsen, S.
History
DepositionMar 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_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

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Assembly

Deposited unit
A: RIBOSE-PHOSPHATE PYROPHOSPHOKINASE
B: RIBOSE-PHOSPHATE PYROPHOSPHOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,34512
Polymers69,8202
Non-polymers1,52410
Water84747
1
A: RIBOSE-PHOSPHATE PYROPHOSPHOKINASE
B: RIBOSE-PHOSPHATE PYROPHOSPHOKINASE
hetero molecules

A: RIBOSE-PHOSPHATE PYROPHOSPHOKINASE
B: RIBOSE-PHOSPHATE PYROPHOSPHOKINASE
hetero molecules

A: RIBOSE-PHOSPHATE PYROPHOSPHOKINASE
B: RIBOSE-PHOSPHATE PYROPHOSPHOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,03536
Polymers209,4616
Non-polymers4,57330
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area33130 Å2
ΔGint-364 kcal/mol
Surface area57320 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)115.600, 115.600, 107.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsThe biological assembly is a homohexamer with 32 point group symmetry

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Components

#1: Protein RIBOSE-PHOSPHATE PYROPHOSPHOKINASE / PHOSPHORIBOSYLDIPHOSPHATE SYNTHETASE


Mass: 34910.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: PRS / Plasmid: PAB600 / Production host: Escherichia coli (E. coli) / Strain (production host): HO773, IV
References: UniProt: P14193, ribose-phosphate diphosphokinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-ABM / METHYL PHOSPHONIC ACID ADENOSINE ESTER / ALPHA-METHYLENE ADENOSINE MONOPHOSPHATE


Mass: 345.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16N5O6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.97 Å3/Da / Density % sol: 58.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: sodium phosphate, alpha, beta methylene ATP, ADP, magnesium chloride, ribose-5-phosphate, ammonium sulfate, TrisHCl, PEG 400. Crystal was soaked in cadmium chloride in phosphate free ...Details: sodium phosphate, alpha, beta methylene ATP, ADP, magnesium chloride, ribose-5-phosphate, ammonium sulfate, TrisHCl, PEG 400. Crystal was soaked in cadmium chloride in phosphate free conditions, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal grow
*PLUS
Details: Bentsen, A.K., (1996) Proteins 24. 238.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
17.7 mg/mlprotein1drop
21.8 mMmATP1drop
32 mMADP1drop
44.4 mMRib-5-P1drop
59.8 mM1dropMg2SO4
650 mMNaPi1droppH7.5
70.5 %beta-octylglucoside1drop
80.1 MTris-HCl1reservoirpH7.5
92.0 Mammonium sulfate1reservoir
102.0 %(v/v)PEG4001reservoir

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Data collection

DiffractionMean temperature: 274 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 1, 2000
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 20019 / Num. obs: 19806 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 39.01 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 4.4
Reflection shellResolution: 2.8→3 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.4 / % possible all: 96.2
Reflection
*PLUS
% possible obs: 98 %
Reflection shell
*PLUS
% possible obs: 96.2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
TRUNCATEdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.273 1996 random
Rwork0.2 --
all0.2 19806 -
obs0.2 19806 -
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4597 0 70 47 4714
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_angle_deg2.103
X-RAY DIFFRACTIONx_improper_angle_d2.137
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / σ(F): 0 / Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_angle_deg1.948
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.137

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