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

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Basic information

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


GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / GTP diphosphokinase / kinase activity / phosphorylation
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
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / GTP pyrophosphokinase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBange, G. / Vogt, M. / Steinchen, W. / 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 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTP pyrophosphokinase
B: GTP pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2476
Polymers56,1882
Non-polymers1,0594
Water54030
1
A: GTP pyrophosphokinase
B: GTP pyrophosphokinase
hetero molecules

A: GTP pyrophosphokinase
B: GTP pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,49512
Polymers112,3774
Non-polymers2,1188
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,-y+3/2,-z+1/41
Buried area13270 Å2
ΔGint-83 kcal/mol
Surface area35670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.862, 125.862, 217.879
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 4.68 Å3/Da / Density % sol: 73.73 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris pH 8.5, 0.2 M lithium sulfate and 30%, 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, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.9→46.46 Å / Num. obs: 19874 / % possible obs: 99.85 % / Redundancy: 11.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.179 / Net I/σ(I): 14.61
Reflection shellResolution: 2.9→3 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 2.15 / Num. unique obs: 1958 / CC1/2: 0.761 / % possible all: 99.24

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FGJ

6fgj


Resolution: 2.9→46.4 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2618 --
Rwork0.2229 --
obs-19868 99.8 %
Refinement stepCycle: LAST / Resolution: 2.9→46.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3206 0 64 30 3300

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