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

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Basic information

Entry
Database: PDB / ID: 1dku
TitleCRYSTAL STRUCTURES OF BACILLUS SUBTILIS PHOSPHORIBOSYLPYROPHOSPHATE SYNTHETASE: MOLECULAR BASIS OF ALLOSTERIC INHIBITION AND ACTIVATION.
ComponentsPROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)
KeywordsTRANSFERASE / OPEN ALPHA-BETA STRUCTURE / DOMAIN DUPLICATION / PHOSPHORIBOSYLTRANSFERASE TYPE I FOLD
Function / homology
Function and homology information


ribonucleoside monophosphate biosynthetic process / ribose phosphate diphosphokinase complex / 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 / PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / Ribose-phosphate pyrophosphokinase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 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: 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 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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: PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)
B: PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3616
Polymers69,8202
Non-polymers1,5414
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-11 kcal/mol
Surface area25050 Å2
MethodPISA
2
A: PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)
B: PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)
hetero molecules

A: PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)
B: PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)
hetero molecules

A: PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)
B: PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,08418
Polymers209,4616
Non-polymers4,62312
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 area32980 Å2
ΔGint-85 kcal/mol
Surface area55980 Å2
MethodPISA
3
A: PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)
hetero molecules

B: PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3616
Polymers69,8202
Non-polymers1,5414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area6060 Å2
ΔGint-19 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.650, 115.650, 106.410
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 PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE) / 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-AP2 / PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER


Mass: 425.228 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17N5O9P2
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.94 Å3/Da / Density % sol: 58.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Sodium citrate, Hepes, alpha,beta-methylene ADP, Magnesium chloride, beta- octylglucoside , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
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: 285 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.912
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 27, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.912 Å / Relative weight: 1
ReflectionResolution: 1.7→23 Å / Num. obs: 83506 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 4.3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.037 / % possible all: 93.4
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 23 Å / Num. obs: 40252 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.35 Å / % possible obs: 98.8 % / Num. unique obs: 7158 / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
TRUNCATEdata scaling
X-PLORphasing
RefinementResolution: 2.2→30 Å / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.241 4093 SELECTED IN CONSISTENCE WITH THE R-FREE DATA FOR STRUCTURE ID CODE 1DKR
Rwork0.198 --
obs0.198 40252 -
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4544 0 100 180 4824
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
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
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 2.011

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