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- PDB-6h5e: Crystal Structure of the GatD/MurT Enzyme Complex from Staphyloco... -

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Basic information

Entry
Database: PDB / ID: 6h5e
TitleCrystal Structure of the GatD/MurT Enzyme Complex from Staphylococcus aureus with bound AMPPNP
Components
  • DUF1727 domain-containing protein
  • SA1707 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 / 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 (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DI(HYDROXYETHYL)ETHER / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT / 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 / MOLECULAR REPLACEMENT / Resolution: 2.139 Å
AuthorsNoeldeke, E.R. / Niemann, V. / Stoerk, E. / 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
DepositionJul 24, 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
Revision 1.2Sep 26, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SA1707 protein
B: DUF1727 domain-containing protein
C: SA1707 protein
D: DUF1727 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,67319
Polymers155,5804
Non-polymers2,09315
Water6,702372
1
A: SA1707 protein
B: DUF1727 domain-containing 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 lead to complex disassembly. See entry 6GS2, SAXS, The ...Evidence: gel filtration, Affinity purification was carried out with only one component affinity tagged. No conditions could be found that lead to complex disassembly. See entry 6GS2, SAXS, The scattering profile is consistent with the size and shape of the heterodimer. Simulated scattering profiles for larger assemblies, such as the entire content of the ASU do not match experimental data. See entry 6GS2
  • 78.4 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)78,3865
Polymers77,7902
Non-polymers5963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: SA1707 protein
D: DUF1727 domain-containing 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 lead to complex disassembly. See entry 6GS2, SAXS, The ...Evidence: gel filtration, Affinity purification was carried out with only one component affinity tagged. No conditions could be found that lead to complex disassembly. See entry 6GS2, SAXS, The scattering profile is consistent with the size and shape of the heterodimer. Simulated scattering profiles for larger assemblies, such as the entire content of the ASU do not match experimental data. See entry 6GS2
  • 79.3 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)79,28714
Polymers77,7902
Non-polymers1,49712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.720, 109.740, 123.300
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 (E. coli) / References: UniProt: A0A0H3JN63
#2: Protein DUF1727 domain-containing protein / Mur ligase middle domain protein / UDP-N-acetylmuramate--alanine ligase / MurT


Mass: 49250.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: BTN44_02275, C3B39_12565, EP54_01845, EQ90_00760, HMPREF3211_01062
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D6HDA2, UniProt: A0A0H3JUU7*PLUS

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Non-polymers , 7 types, 387 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.57 Å3/Da / Density % sol: 52.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9.1
Details: 100 mM Tris pH 9.1 350 mM MgCl2 18 % PEG 8000 13 % Glycerol

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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: Feb 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.139→50 Å / Num. obs: 82581 / % possible obs: 99.8 % / Redundancy: 13.5 % / Biso Wilson estimate: 51.9 Å2 / CC1/2: 1 / Rpim(I) all: 0.031 / Rrim(I) all: 0.116 / Net I/av σ(I): 19.36 / Net I/σ(I): 19.37
Reflection shellResolution: 2.139→2.216 Å / Redundancy: 12.6 % / Mean I/σ(I) obs: 1.23 / Num. unique obs: 8030 / CC1/2: 0.847 / Rpim(I) all: 0.661 / Rrim(I) all: 2.369 / % possible all: 97.95

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSVersion May1, 2016data reduction
XDSVersion May1, 2016data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GS2

6gs2


Resolution: 2.139→49.075 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.32
RfactorNum. reflection% reflection
Rfree0.2354 1504 1.82 %
Rwork0.1919 --
obs0.1927 82478 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.139→49.075 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9807 0 120 372 10299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110149
X-RAY DIFFRACTIONf_angle_d1.42413742
X-RAY DIFFRACTIONf_dihedral_angle_d18.1823665
X-RAY DIFFRACTIONf_chiral_restr0.071549
X-RAY DIFFRACTIONf_plane_restr0.0061776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1391-2.20820.41411350.35877121X-RAY DIFFRACTION98
2.2082-2.28710.34311350.3077341X-RAY DIFFRACTION100
2.2871-2.37870.32751360.27157245X-RAY DIFFRACTION100
2.3787-2.48690.28461340.24287282X-RAY DIFFRACTION100
2.4869-2.6180.32521340.23187337X-RAY DIFFRACTION100
2.618-2.78210.28181370.21837315X-RAY DIFFRACTION100
2.7821-2.99680.2491370.21167358X-RAY DIFFRACTION100
2.9968-3.29840.25731360.19457368X-RAY DIFFRACTION100
3.2984-3.77550.23471380.17127407X-RAY DIFFRACTION100
3.7755-4.75610.17091380.14667476X-RAY DIFFRACTION100
4.7561-49.08830.20921440.17757724X-RAY DIFFRACTION100

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