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- PDB-7r8q: Closed form of SAOUHSC_02373 in complex with ADP, citrate, Mg2+ a... -

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Basic information

Entry
Database: PDB / ID: 7r8q
TitleClosed form of SAOUHSC_02373 in complex with ADP, citrate, 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 / CITRIC ACID / L-aspartate--L-methionine ligase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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 1.2Oct 18, 2023Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)95,67016
Polymers93,8602
Non-polymers1,80914
Water7,945441
1
A: ATP-grasp domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6437
Polymers46,9301
Non-polymers7136
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ATP-grasp domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0279
Polymers46,9301
Non-polymers1,0978
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)145.868, 82.812, 107.782
Angle α, β, γ (deg.)90.000, 131.060, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ATP-grasp domain-containing protein


Mass: 46930.203 Da / Num. of mol.: 2
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, 455 molecules

#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 1.6 M sodium citrate tribasic dihydrate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→36.89 Å / Num. obs: 64488 / % possible obs: 98.7 % / Redundancy: 7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.056 / Rrim(I) all: 0.148 / Net I/σ(I): 9
Reflection shell

Diffraction-ID: 1 / Redundancy: 6.6 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.051.4922945344670.6450.6281.6211.597.9
9.17-36.890.04946407020.9980.020.05327.898.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.18.2-3874refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7R8P

7r8p


Resolution: 2→36.89 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2199 3389 5.26 %
Rwork0.1913 61046 -
obs0.1928 64435 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.09 Å2 / Biso mean: 40.4317 Å2 / Biso min: 23.7 Å2
Refinement stepCycle: final / Resolution: 2→36.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6217 0 114 441 6772
Biso mean--36.3 41.58 -
Num. residues----776
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.02860.38781470.3142251198
2.0286-2.05890.29351260.3092251498
2.0589-2.0910.32751360.2904252198
2.091-2.12530.32651580.2739249498
2.1253-2.16190.30011300.2612252698
2.1619-2.20130.30521420.249249498
2.2013-2.24360.32341340.2466250898
2.2436-2.28940.27751410.2426254498
2.2894-2.33910.24931460.2211252898
2.3391-2.39350.27531310.2206255798
2.3935-2.45340.27581590.2245248198
2.4534-2.51970.24621530.2167254698
2.5197-2.59380.25871400.2158250999
2.5938-2.67750.22771240.2237256499
2.6775-2.77320.2811420.2235255299
2.7732-2.88420.27661290.2288254999
2.8842-3.01540.26351420.2195254599
3.0154-3.17430.2431570.2166254099
3.1743-3.37310.21821310.1922259399
3.3731-3.63330.19131290.1653257599
3.6333-3.99850.18321270.1585260099
3.9985-4.57620.16541630.1384255599
4.5762-5.7620.17741500.14092592100
5.762-36.890.16411520.1635264899

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