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- PDB-6fgj: Crystal structure of the small alarmone synthethase 2 from Staphy... -

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Basic information

Entry
Database: PDB / ID: 6fgj
TitleCrystal structure of the small alarmone synthethase 2 from Staphylococcus aureus
ComponentsGTP pyrophosphokinase
KeywordsTRANSFERASE / Stringent response / alarmone / RelP / SAS2 / MRSA
Function / homology
Function and homology information


GTP diphosphokinase / GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / kinase activity / GTP binding / metal ion binding
Similarity search - Function
: / Region found in RelA / SpoT proteins / RelA/SpoT / Region found in RelA / SpoT proteins / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / GTP pyrophosphokinase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.251 Å
AuthorsBange, G. / Steinchen, W. / Vogt, M. / Altegoer, F.
CitationJournal: Sci Rep / Year: 2018
Title: Structural and mechanistic divergence of the small (p)ppGpp synthetases RelP and RelQ.
Authors: Steinchen, W. / Vogt, M.S. / Altegoer, F. / Giammarinaro, P.I. / Horvatek, P. / Wolz, C. / Bange, G.
History
DepositionJan 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 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 1.3Jan 17, 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
A: GTP pyrophosphokinase
B: GTP pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4894
Polymers56,1882
Non-polymers3002
Water59433
1
A: GTP pyrophosphokinase
hetero molecules

A: GTP pyrophosphokinase
hetero molecules

B: GTP pyrophosphokinase
hetero molecules

B: GTP pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,9778
Polymers112,3774
Non-polymers6014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation4_545y+1/2,-x-1/2,z+1/41
crystal symmetry operation5_454-x-1/2,y+1/2,-z-1/41
2
B: GTP pyrophosphokinase
hetero molecules

B: GTP pyrophosphokinase
hetero molecules

A: GTP pyrophosphokinase
hetero molecules

A: GTP pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,9778
Polymers112,3774
Non-polymers6014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_444-y-1,-x-1,-z-1/21
crystal symmetry operation3_444-y-1/2,x-1/2,z-1/41
crystal symmetry operation5_444-x-1/2,y-1/2,-z-1/41
Buried area10680 Å2
ΔGint-54 kcal/mol
Surface area37580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.802, 71.802, 190.828
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein GTP pyrophosphokinase / GTP pyrophosphokinase ywaC / RelA/SpoT domain protein


Mass: 28094.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: ywaC, AB454_12730, AB466_12625, AB478_12605, AB526_12980, AFO97_10970, AFP37_10975, EP54_00695, EQ90_03295, ERS072738_01254, ERS074020_00750, HMPREF3211_00175
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W8U368, GTP diphosphokinase
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H14O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris pH 8.5, 0.2 M lithium sulfate, 30% (w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.25→49.06 Å / Num. obs: 24257 / % possible obs: 99 % / Redundancy: 4.3 % / CC1/2: 1 / Rmerge(I) obs: 0.0364 / Net I/σ(I): 20.37
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.58 / Num. unique obs: 10417 / CC1/2: 0.85 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DEC

5dec


Resolution: 2.251→49.06 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.03
RfactorNum. reflection% reflection
Rfree0.2482 1226 5.06 %
Rwork0.1997 --
obs0.2022 24250 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.251→49.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3261 0 20 33 3314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013352
X-RAY DIFFRACTIONf_angle_d1.2674508
X-RAY DIFFRACTIONf_dihedral_angle_d15.8352074
X-RAY DIFFRACTIONf_chiral_restr0.077516
X-RAY DIFFRACTIONf_plane_restr0.007568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2507-2.34090.35961210.2882467X-RAY DIFFRACTION98
2.3409-2.44740.33011220.25332535X-RAY DIFFRACTION100
2.4474-2.57640.30371240.2292537X-RAY DIFFRACTION99
2.5764-2.73780.30281410.24552520X-RAY DIFFRACTION99
2.7378-2.94920.27861270.25022561X-RAY DIFFRACTION100
2.9492-3.24590.31941500.2352514X-RAY DIFFRACTION98
3.2459-3.71550.25781370.19882597X-RAY DIFFRACTION100
3.7155-4.68050.24641630.16732559X-RAY DIFFRACTION98
4.6805-49.07640.1891410.18122734X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.06190.8608-0.22921.6897-0.13842.02760.01890.0848-0.16530.0327-0.063-0.16230.0980.0692-0.00070.4021-0.0208-0.06860.42260.02330.3811-16.5939-15.9181-14.7986
22.0369-0.09720.69272.0012-0.07691.56920.01240.09520.5155-0.2847-0.14750.1032-0.4945-0.2165-0.0030.69530.1792-0.06940.4694-0.12480.584-31.9687-20.0876-42.3984
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 1:229)
2X-RAY DIFFRACTION2(chain B and resseq 32:229)

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