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- PDB-1dkr: CRYSTAL STRUCTURES OF BACILLUS SUBTILIS PHOSPHORIBOSYLPYROPHOSPHA... -

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Basic information

Entry
Database: PDB / ID: 1dkr
TitleCRYSTAL STRUCTURES OF BACILLUS SUBTILIS PHOSPHORIBOSYLPYROPHOSPHATE SYNTHETASE: MOLECULAR BASIS OF ALLOSTERIC INHIBITION AND ACTIVATION.
ComponentsPHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASERibose-phosphate diphosphokinase
KeywordsTRANSFERASE / DOMAIN DUPLICATION / OPEN ALPHA BETA DOMAIN STRUCTURE / PHOSPHORIBOSYLTRANSFERASE TYPE I FOLD.
Function / homology
Function and homology information


ribose phosphate diphosphokinase complex / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / ribonucleoside monophosphate biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / purine nucleotide biosynthetic process / kinase activity / phosphorylation / magnesium ion binding / ATP binding / 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
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsEriksen, T.A. / Kadziola, A. / Bentsen, A.-K. / Harlow, K.W. / Larsen, S.
Citation
Journal: Nat.Struct.Biol. / Year: 2000
Title: Structural basis for the function of Bacillus subtilis phosphoribosyl-pyrophosphate synthetase.
Authors: Eriksen, T.A. / Kadziola, A. / Bentsen, A.K. / Harlow, K.W. / Larsen, S.
#1: Journal: Proteins / Year: 1996
Title: Overexpression of the B. Subtilis Phosphoribosylpyrophosphate Synthetase and Crystallization of the Free Enzyme and its Substrate-Effector Complexes
Authors: Bentsen, A.-K. / Larsen, T.A. / Kadziola, A. / Larsen, S. / Harlow, K.W.
History
DepositionDec 8, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2000Provider: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE
B: PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2056
Polymers69,8202
Non-polymers3844
Water4,143230
1
A: PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE
B: PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE
hetero molecules

A: PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE
B: PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE
hetero molecules

A: PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE
B: PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,61418
Polymers209,4616
Non-polymers1,15312
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 area28000 Å2
ΔGint-260 kcal/mol
Surface area60470 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)115.610, 115.610, 107.750
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE / Ribose-phosphate diphosphokinase / RIBOSE-PHOSPHATE PYROPHOSPHOKINASE


Mass: 34910.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / 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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.98 Å3/Da / Density % sol: 58.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: AMMONIUM SULFATE; TRISHCL; PEG 400; SODIUM PHOSPHATE; BETA-OCTYLGLUCOSIDE; ALPHA, BETA-METHYLENE ATP; RIBOSE-5-PHOSPHATE; MAGNESIUM SULFATE; ADP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlprotein1drop
225 mMmADP1drop
350 mM1dropMgCl2
40.5 %(w/v)beta-octylglucoside1drop
51 Msodium citrate1reservoir
60.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 274 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: May 23, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. all: 40947 / Num. obs: 40947 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.2 / % possible all: 99.6
Reflection
*PLUS
Num. obs: 35812 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 99.6 % / Num. unique obs: 5098 / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.6

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Processing

Software
NameVersionClassification
MLPHAREphasing
DMmodel building
X-PLOR3.1refinement
DENZOdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
TRUNCATEdata scaling
DMphasing
RefinementResolution: 2.3→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.24 3610 RANDOMLY WITHIN RESOLUTION SHELL
Rwork0.18 --
obs0.18 35645 -
all-35645 -
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4658 0 20 230 4908
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d1.799
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.18 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg2.134

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