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- PDB-7r8p: Open form of SAOUHSC_02373 in complex with ADP, Mg2+ and Na+ -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7r8p
TitleOpen form of SAOUHSC_02373 in complex with ADP, Mg2+ and Na+
ComponentsATP-grasp domain-containing protein
KeywordsLIGASE / ATP-grasp superfamily / L-amino acid ligase
Function / homology
Function and homology information


L-amino-acid alpha-ligase activity / sulfur amino acid metabolic process / alpha-amino acid metabolic process / acid-amino acid ligase activity / methionine metabolic process / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / magnesium ion binding / protein homodimerization activity / ATP binding / identical protein binding
Similarity search - Function
: / ATP-grasp fold / ATP-grasp fold profile.
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / L-aspartate--L-methionine ligase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.37 Å
AuthorsPederick, J.L. / Bruning, J.B.
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Discovery of an ʟ-amino acid ligase implicated in Staphylococcal sulfur amino acid metabolism.
Authors: Pederick, J.L. / Horsfall, A.J. / Jovcevski, B. / Klose, J. / Abell, A.D. / Pukala, T.L. / Bruning, J.B.
History
DepositionJun 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-grasp domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4405
Polymers46,9301
Non-polymers5104
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.258, 70.581, 109.773
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ATP-grasp domain-containing protein


Mass: 46930.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria)
Strain: NCTC 8325 / PS 47 / Gene: SAOUHSC_02373 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2FWC5

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Non-polymers , 5 types, 382 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 1.99 Å3/Da / Density % sol: 38.25 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 200 mM sodium acetate trihydrate, 100 mM Tris-HCl pH 8.5, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.37→39.84 Å / Num. obs: 79614 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.017 / Rrim(I) all: 0.062 / Net I/σ(I): 18 / Num. measured all: 1057862 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.37-1.39121.6544661238890.6430.4951.7281.6100
7.5-39.8411.50.03865955740.9990.0110.0452.898.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.18.2-3874refinement
XDSdata reduction
Aimless0.7.4data scaling
Fragon0.2.4phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2 ideal alpha helices of 10aa

10aa


Resolution: 1.37→37.45 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.215 3929 4.94 %
Rwork0.1903 75593 -
obs0.1915 79522 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.75 Å2 / Biso mean: 27.7248 Å2 / Biso min: 14.09 Å2
Refinement stepCycle: final / Resolution: 1.37→37.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2931 0 30 378 3339
Biso mean--20.49 38.91 -
Num. residues----364
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.37-1.390.32421330.299226612794
1.39-1.40.30661250.283826982823
1.4-1.420.31321460.279726702816
1.42-1.440.30731550.267226042759
1.44-1.460.30181540.258126962850
1.46-1.480.26311390.249426222761
1.48-1.510.31861370.23526992836
1.51-1.530.28391370.240126792816
1.53-1.560.24031340.225126742808
1.56-1.590.26941300.225426532783
1.59-1.620.25981440.225126852829
1.62-1.650.2041240.220826762800
1.65-1.690.26631490.216126832832
1.69-1.730.23641370.213827032840
1.73-1.770.21391500.213926492799
1.77-1.820.21951560.202726752831
1.82-1.870.23761490.201926832832
1.87-1.930.24631320.209627162848
1.93-20.23481500.204526632813
2-2.080.21961250.20527202845
2.08-2.170.22221540.194526932847
2.17-2.290.21831440.193427182862
2.29-2.430.22171170.190927392856
2.43-2.620.22471460.201227062852
2.62-2.880.23291440.197927322876
2.88-3.30.19441410.182927632904
3.3-4.160.16931390.152928022941
4.16-37.450.19471380.16829313069

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