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- PDB-5ded: Crystal structure of the small alarmone synthethase 1 from Bacill... -

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Basic information

Entry
Database: PDB / ID: 5ded
TitleCrystal structure of the small alarmone synthethase 1 from Bacillus subtilis bound to its product pppGpp
ComponentsGTP pyrophosphokinase YjbM
KeywordsTRANSFERASE / (p)ppGpp / alarmone / stringent response / allosteric regulator
Function / homology
Function and homology information


GTP diphosphokinase / GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / kinase activity / GTP binding / ATP binding / metal ion binding
Similarity search - Function
Nucleotidyltransferase / : / Region found in RelA / SpoT proteins / RelA/SpoT / Region found in RelA / SpoT proteins / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / Helix Hairpins / 2-Layer Sandwich ...Nucleotidyltransferase / : / Region found in RelA / SpoT proteins / RelA/SpoT / Region found in RelA / SpoT proteins / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-0O2 / GTP pyrophosphokinase YjbM
Similarity search - Component
Biological speciesBacillus subtilis PY79 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.942 Å
AuthorsSteinchen, W. / Schuhmacher, J.S. / Altegoer, F. / Bange, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Catalytic mechanism and allosteric regulation of an oligomeric (p)ppGpp synthetase by an alarmone.
Authors: Steinchen, W. / Schuhmacher, J.S. / Altegoer, F. / Fage, C.D. / Srinivasan, V. / Linne, U. / Marahiel, M.A. / Bange, G.
History
DepositionAug 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: GTP pyrophosphokinase YjbM
A: GTP pyrophosphokinase YjbM
B: GTP pyrophosphokinase YjbM
C: GTP pyrophosphokinase YjbM
E: GTP pyrophosphokinase YjbM
F: GTP pyrophosphokinase YjbM
G: GTP pyrophosphokinase YjbM
H: GTP pyrophosphokinase YjbM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,32924
Polymers205,0348
Non-polymers8,29516
Water00
1
D: GTP pyrophosphokinase YjbM
B: GTP pyrophosphokinase YjbM
F: GTP pyrophosphokinase YjbM
G: GTP pyrophosphokinase YjbM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,66512
Polymers102,5174
Non-polymers4,1478
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11140 Å2
ΔGint-96 kcal/mol
Surface area35640 Å2
MethodPISA
2
A: GTP pyrophosphokinase YjbM
C: GTP pyrophosphokinase YjbM
E: GTP pyrophosphokinase YjbM
H: GTP pyrophosphokinase YjbM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,66512
Polymers102,5174
Non-polymers4,1478
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11440 Å2
ΔGint-98 kcal/mol
Surface area36070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.869, 113.492, 139.848
Angle α, β, γ (deg.)90.00, 127.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
GTP pyrophosphokinase YjbM / (p)ppGpp synthase YjbM / Small alarmone synthase 1 / SAS 1


Mass: 25629.303 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis PY79 (bacteria) / Strain: 168 / Gene: yjbM, BSU11600 / Plasmid: pET24d(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O31611, GTP diphosphokinase
#2: Chemical
ChemComp-0O2 / guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate)


Mass: 683.140 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H18N5O20P5
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Citric acid, pH 4.0, 5% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97934 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.94→50.6 Å / Num. obs: 51454 / % possible obs: 96.1 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 5.8
Reflection shellRmerge(I) obs: 0.273

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DEC

5dec


Resolution: 2.942→50.567 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2449 2634 5.12 %
Rwork0.1805 --
obs0.1838 51454 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.942→50.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12532 0 484 0 13016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01413269
X-RAY DIFFRACTIONf_angle_d1.44118015
X-RAY DIFFRACTIONf_dihedral_angle_d22.1685261
X-RAY DIFFRACTIONf_chiral_restr0.0751926
X-RAY DIFFRACTIONf_plane_restr0.0062211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9424-2.99590.31571210.22042236X-RAY DIFFRACTION84
2.9959-3.05350.28211450.22480X-RAY DIFFRACTION97
3.0535-3.11580.32561260.19582519X-RAY DIFFRACTION97
3.1158-3.18360.31881390.19412555X-RAY DIFFRACTION98
3.1836-3.25760.23921280.19382592X-RAY DIFFRACTION99
3.2576-3.3390.33271390.18362582X-RAY DIFFRACTION98
3.339-3.42930.26561300.18152567X-RAY DIFFRACTION99
3.4293-3.53020.28951420.18242572X-RAY DIFFRACTION99
3.5302-3.64410.2351580.17342560X-RAY DIFFRACTION99
3.6441-3.77430.26811400.17612594X-RAY DIFFRACTION99
3.7743-3.92540.22971410.18952624X-RAY DIFFRACTION99
3.9254-4.10390.22751500.17522569X-RAY DIFFRACTION100
4.1039-4.32020.21321410.16752606X-RAY DIFFRACTION100
4.3202-4.59070.21061450.14462608X-RAY DIFFRACTION100
4.5907-4.94490.19781520.15212621X-RAY DIFFRACTION100
4.9449-5.4420.23021340.18272631X-RAY DIFFRACTION100
5.442-6.22820.24131520.19172595X-RAY DIFFRACTION100
6.2282-7.84220.24511230.20352669X-RAY DIFFRACTION100
7.8422-50.57460.22941280.18842640X-RAY DIFFRACTION97

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