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- PDB-6gs2: Crystal Structure of the GatD/MurT Enzyme Complex from Staphyloco... -

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Basic information

Entry
Database: PDB / ID: 6gs2
TitleCrystal Structure of the GatD/MurT Enzyme Complex from Staphylococcus aureus
Components
  • SA1707 protein
  • SA1708 protein
KeywordsBIOSYNTHETIC PROTEIN / cell wall biosynthesis / peptidoglycan / antibiotic resistance
Function / homology
Function and homology information


lipid II isoglutaminyl synthase (glutamine-hydrolysing) / carbon-nitrogen ligase activity on lipid II / acid-amino acid ligase activity / glutaminase / cobalamin biosynthetic process / glutaminase activity / glutamine metabolic process / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape ...lipid II isoglutaminyl synthase (glutamine-hydrolysing) / carbon-nitrogen ligase activity on lipid II / acid-amino acid ligase activity / glutaminase / cobalamin biosynthetic process / glutaminase activity / glutamine metabolic process / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / zinc ion binding / ATP binding
Similarity search - Function
Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT, C-terminal / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT / MurT ligase C-terminal / CobB/CobQ-like glutamine amidotransferase / Cobyric acid synthase, glutamine amidotransferase type 1 / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD / CobB/CobQ-like glutamine amidotransferase domain / CobBQ-type GATase domain profile. / Mur ligase, central / Mur-like, catalytic domain superfamily ...Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT, C-terminal / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT / MurT ligase C-terminal / CobB/CobQ-like glutamine amidotransferase / Cobyric acid synthase, glutamine amidotransferase type 1 / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD / CobB/CobQ-like glutamine amidotransferase domain / CobBQ-type GATase domain profile. / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / Class I glutamine amidotransferase-like
Similarity search - Domain/homology
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / DI(HYDROXYETHYL)ETHER / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.04 Å
AuthorsMuckenfuss, L.M. / Noeldeke, E.R. / Niemann, V. / Zocher, G. / Stehle, T.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationDFG-SFB-766 Germany
German Research FoundationDFG-SFB-TR34 Germany
CitationJournal: Sci Rep / Year: 2018
Title: Structural basis of cell wall peptidoglycan amidation by the GatD/MurT complex of Staphylococcus aureus.
Authors: Noldeke, E.R. / Muckenfuss, L.M. / Niemann, V. / Muller, A. / Stork, E. / Zocher, G. / Schneider, T. / Stehle, T.
History
DepositionJun 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / 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_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SA1707 protein
B: SA1708 protein
C: SA1707 protein
D: SA1708 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,9649
Polymers155,5804
Non-polymers3835
Water11,043613
1
A: SA1707 protein
B: SA1708 protein
hetero molecules


  • defined by author
  • Evidence: gel filtration, Affinity purification was carried out with only one component affinity tagged. No conditions could be found that led to complex disassembly., SAXS, The scattering profile is ...Evidence: gel filtration, Affinity purification was carried out with only one component affinity tagged. No conditions could be found that led to complex disassembly., SAXS, The scattering profile is consistent with the size of the heterodimer. Simulated scattering profiles from larger assemblies as observed in crystal contacts do not match the experimental data.
  • 78.1 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)78,1086
Polymers77,7902
Non-polymers3184
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: SA1707 protein
D: SA1708 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8553
Polymers77,7902
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.100, 110.370, 116.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein SA1707 protein / GatD


Mass: 28539.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: N315 / Gene: SA1707 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3JN63
#2: Protein SA1708 protein / MurT


Mass: 49250.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain N315) (bacteria)
Strain: N315 / Gene: SA1708 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3JUU7

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Non-polymers , 5 types, 618 molecules

#3: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 613 / 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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 100 mM Tris pH 8.6, 40% (w/v) PEG 8000, 350 mM magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.04→49.07 Å / Num. obs: 88009 / % possible obs: 99.7 % / Redundancy: 7.3 % / Biso Wilson estimate: 33.3 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.042 / Rrim(I) all: 0.113 / Net I/σ(I): 14.6
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 8685 / CC1/2: 0.714 / Rpim(I) all: 0.604 / Rrim(I) all: 1.634 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
REFMAC5.8.0049refinement
XDSVERSION May 1, 2016data reduction
XSCALEVERSION May 1, 2016data scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.04→49.056 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.73
RfactorNum. reflection% reflection
Rfree0.2156 1503 1.71 %
Rwork0.1753 --
obs0.176 87852 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.04→49.056 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9724 0 18 613 10355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110097
X-RAY DIFFRACTIONf_angle_d1.32713668
X-RAY DIFFRACTIONf_dihedral_angle_d18.1093665
X-RAY DIFFRACTIONf_chiral_restr0.0641541
X-RAY DIFFRACTIONf_plane_restr0.0061778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.10580.45381340.43767616X-RAY DIFFRACTION98
2.1058-2.18110.29611340.25797780X-RAY DIFFRACTION100
2.1811-2.26840.37921350.32027632X-RAY DIFFRACTION97
2.2684-2.37170.25681460.20367750X-RAY DIFFRACTION100
2.3717-2.49670.2171180.18567854X-RAY DIFFRACTION100
2.4967-2.65310.25981490.17697828X-RAY DIFFRACTION100
2.6531-2.85790.20351370.1737841X-RAY DIFFRACTION100
2.8579-3.14550.22711360.16947916X-RAY DIFFRACTION100
3.1455-3.60050.20831400.14997900X-RAY DIFFRACTION100
3.6005-4.53580.15591340.12617987X-RAY DIFFRACTION100
4.5358-49.06990.17941400.15998245X-RAY DIFFRACTION100

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