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- PDB-5mp7: Crystal structure of phosphoribosylpyrophosphate synthetase from ... -

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Basic information

Entry
Database: PDB / ID: 5mp7
TitleCrystal structure of phosphoribosylpyrophosphate synthetase from Mycobacterium smegmatis
ComponentsRibose-phosphate pyrophosphokinase
KeywordsTRANSFERASE / phosphoribosylpyrophosphate synthetase / PRPP synthetase / Mycobacterium smegmatis
Function / homology
Function and homology information


ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / ribonucleoside monophosphate biosynthetic process / nucleotide biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / nucleoside metabolic 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 / Ribose-phosphate pyrophosphokinase / Ribose-phosphate pyrophosphokinase, N-terminal domain / N-terminal domain of ribose phosphate pyrophosphokinase / Rossmann fold - #2020 / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain ...Phosphoribosyl pyrophosphate synthetase, conserved site / Phosphoribosyl pyrophosphate synthase signature. / Ribose-phosphate pyrophosphokinase, bacterial-type / 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
ACETATE ION / Ribose-phosphate pyrophosphokinase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDonini, S. / Garavaglia, S. / Ferraris, D.M. / Miggiano, R. / Mori, S. / Shibayama, K. / Rizzi, M.
Funding support Italy, 1items
OrganizationGrant numberCountry
EU 7th Framework Program260872 Italy
CitationJournal: PLoS ONE / Year: 2017
Title: Biochemical and structural investigations on phosphoribosylpyrophosphate synthetase from Mycobacterium smegmatis.
Authors: Donini, S. / Garavaglia, S. / Ferraris, D.M. / Miggiano, R. / Mori, S. / Shibayama, K. / Rizzi, M.
History
DepositionDec 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_close_contact ...pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.2Jul 13, 2022Group: Database references / Structure summary / Category: audit_author / database_2
Item: _audit_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
C: Ribose-phosphate pyrophosphokinase
B: Ribose-phosphate pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,9886
Polymers106,8113
Non-polymers1773
Water1,22568
1
A: Ribose-phosphate pyrophosphokinase
C: Ribose-phosphate pyrophosphokinase
B: Ribose-phosphate pyrophosphokinase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)213,97612
Polymers213,6216
Non-polymers3546
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area16240 Å2
ΔGint-63 kcal/mol
Surface area69840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.292, 85.292, 249.791
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22B
13C
23B

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 0 / Auth seq-ID: 10 - 316 / Label seq-ID: 10 - 316

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21CB
12AA
22BC
13CB
23BC

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Ribose-phosphate pyrophosphokinase / RPPK / 5-phospho-D-ribosyl alpha-1-diphosphate / Phosphoribosyl diphosphate synthase / ...RPPK / 5-phospho-D-ribosyl alpha-1-diphosphate / Phosphoribosyl diphosphate synthase / Phosphoribosyl pyrophosphate synthase


Mass: 35603.562 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Gene: prs, MSMEG_5427, MSMEI_5278 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0R3C8, ribose-phosphate diphosphokinase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2M NaCl, 0.1M Sodium acetate, 30% (v/v) 2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→43.38 Å / Num. obs: 35723 / % possible obs: 96.18 % / Redundancy: 1.9 % / Biso Wilson estimate: 38.07 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 6.24
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.34 / % possible all: 97.26

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DKR

1dkr


Resolution: 2.4→50.01 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.942 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 0.524 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 1820 5.1 %RANDOM
Rwork0.19817 ---
obs0.1996 33860 96.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.983 Å2
Baniso -1Baniso -2Baniso -3
1--2.53 Å20 Å20 Å2
2---2.53 Å2-0 Å2
3---5.06 Å2
Refinement stepCycle: 1 / Resolution: 2.4→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6864 0 12 68 6944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196990
X-RAY DIFFRACTIONr_bond_other_d0.0070.026876
X-RAY DIFFRACTIONr_angle_refined_deg1.651.9649468
X-RAY DIFFRACTIONr_angle_other_deg1.549315756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1865888
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.10723.558312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.216151188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2781563
X-RAY DIFFRACTIONr_chiral_restr0.0860.21098
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217914
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021557
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1333.8793573
X-RAY DIFFRACTIONr_mcbond_other3.1193.8773569
X-RAY DIFFRACTIONr_mcangle_it4.8315.8124452
X-RAY DIFFRACTIONr_mcangle_other4.835.8124453
X-RAY DIFFRACTIONr_scbond_it5.0474.6543417
X-RAY DIFFRACTIONr_scbond_other5.0474.6543418
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1466.6715017
X-RAY DIFFRACTIONr_long_range_B_refined12.15937.79327958
X-RAY DIFFRACTIONr_long_range_B_other12.15937.79427955
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A355360.1
12C355360.1
21A353860.11
22B353860.11
31C352340.11
32B352340.11
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 117 -
Rwork0.298 2484 -
obs--97.2 %

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