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

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Basic information

Entry
Database: PDB / ID: 6ewz
TitleCrystal structure of RelP (SAS2) from Staphylococcus aureus bound to AMPCPP and GTP in the pre-catalytic state
ComponentsGTP pyrophosphokinase
KeywordsTRANSFERASE / magic spot / (p)ppGpp / small alarmone synthetase / persistence / resistance / MRSA / staphylococcus
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
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / : / GUANOSINE-5'-TRIPHOSPHATE / GTP pyrophosphokinase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 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 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _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_conn.ptnr2_label_seq_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)58,3509
Polymers56,1882
Non-polymers2,1617
Water1,78399
1
A: GTP pyrophosphokinase
B: GTP pyrophosphokinase
hetero molecules

A: GTP pyrophosphokinase
B: GTP pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,69918
Polymers112,3774
Non-polymers4,32214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+3/2,y,-z+3/41
Buried area18250 Å2
ΔGint-125 kcal/mol
Surface area36360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.120, 125.120, 219.070
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

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Protein , 1 types, 2 molecules AB

#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, BER48_002454, CEJ93_03805, ERS072738_01254, ERS073583_01544, ERS074020_00750, HMPREF3211_00175
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W8U368, GTP diphosphokinase

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Non-polymers , 5 types, 106 molecules

#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-FE / FE (III) ION


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


Mass: 18.015 Da / Num. of mol.: 99 / 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: 3.81 Å3/Da / Density % sol: 67.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris-HCl pH8.5 25% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.24→63.07 Å / Num. obs: 42049 / % possible obs: 99.93 % / Redundancy: 13.2 % / CC1/2: 1 / Rmerge(I) obs: 0.05537 / Rpim(I) all: 0.01592 / Rrim(I) all: 0.05765 / Net I/σ(I): 24.81
Reflection shellResolution: 2.24→2.32 Å / Redundancy: 13.1 % / Rmerge(I) obs: 1.811 / Mean I/σ(I) obs: 1.42 / CC1/2: 0.664 / Rpim(I) all: 0.5174 / Rrim(I) all: 1.885 / % possible all: 99.88

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Processing

Software
NameClassification
PHENIXrefinement
xia2data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ded

5ded


Resolution: 2.24→63.07 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2335 2100 5 %
Rwork0.1925 --
obs0.1946 42042 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.24→63.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3304 0 129 92 3525
LS refinement shellResolution: 2.24→2.92 Å
Num. reflection% reflection
Rwork42042 -
Rfree-5 %
obs-100 %

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