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- PDB-6ex0: Crystal structure of RelP (SAS2) from Staphylococcus aureus bound... -

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Basic information

Entry
Database: PDB / ID: 6ex0
TitleCrystal structure of RelP (SAS2) from Staphylococcus aureus bound to pppGpp in the post-catalytic state
ComponentsGTP pyrophosphokinase
KeywordsTRANSFERASE / stringent response / (p)ppGpp / persistence / small alarmone synthetase
Function / homology
Function and homology information


GTP diphosphokinase activity / GTP diphosphokinase / 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
Chem-0O2 / : / GTP pyrophosphokinase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsManav, M.C. / Brodersen, D.E.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish National Research FoundationDNRF120 Denmark
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural basis for (p)ppGpp synthesis by theStaphylococcus aureussmall alarmone synthetase RelP.
Authors: Manav, M.C. / Beljantseva, J. / Bojer, M.S. / Tenson, T. / Ingmer, H. / Hauryliuk, V. / Brodersen, D.E.
History
DepositionNov 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 2.0Sep 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_comp_id_1 / _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 / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)57,6105
Polymers56,1882
Non-polymers1,4223
Water45025
1
A: GTP pyrophosphokinase
B: GTP pyrophosphokinase
hetero molecules

A: GTP pyrophosphokinase
B: GTP pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,22110
Polymers112,3774
Non-polymers2,8446
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+3/2,y,-z+3/41
Buried area10590 Å2
ΔGint-88 kcal/mol
Surface area36820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.330, 124.330, 213.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

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


Mass: 28094.137 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-0O2 / guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate)


Mass: 683.140 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H18N5O20P5
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.78 Å3/Da / Density % sol: 67.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Hepes-Na pH7.0 0.2M Sodium thiocyanate 40% pentaerythriol propoxylate (5/4 PO/OH)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.78→53.7 Å / Num. obs: 133228 / % possible obs: 99.31 % / Redundancy: 6.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.07323 / Rpim(I) all: 0.03043 / Rrim(I) all: 0.07981 / Net I/σ(I): 12.63
Reflection shellResolution: 2.78→2.879 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.048 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 10390 / CC1/2: 0.53 / Rpim(I) all: 0.4922 / Rrim(I) all: 1.168 / % possible all: 93.11

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Processing

Software
NameVersionClassification
PHENIX(dev_2614: ???)refinement
xia2data reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DED

5ded


Resolution: 2.78→53.7 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2631 1049 4.93 %
Rwork0.2177 --
obs0.22 133228 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 88.77 Å2
Refinement stepCycle: LAST / Resolution: 2.78→53.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3240 0 81 25 3346
LS refinement shellResolution: 2.78→2.92 Å /
Num. reflection% reflection
Rwork21285 -
obs-22 %

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