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- PDB-4k9s: Peptidoglycan O-acetylesterase in action, setmet -

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Basic information

Entry
Database: PDB / ID: 4k9s
TitlePeptidoglycan O-acetylesterase in action, setmet
ComponentsGDSL-like Lipase/Acylhydrolase family protein
KeywordsHYDROLASE / Alpha/Beta Fold / Peptidoglycan hydrolase
Function / homologyJelly Rolls - #1360 / SGNH hydrolase / Jelly Rolls / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta / :
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.334 Å
AuthorsWilliams, A.H. / Gompert Boneca, I.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Visualization of a substrate-induced productive conformation of the catalytic triad of the Neisseria meningitidis peptidoglycan O-acetylesterase reveals mechanistic conservation in SGNH esterase family members.
Authors: Williams, A.H. / Veyrier, F.J. / Bonis, M. / Michaud, Y. / Raynal, B. / Taha, M.K. / White, S.W. / Haouz, A. / Boneca, I.G.
History
DepositionApr 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GDSL-like Lipase/Acylhydrolase family protein
B: GDSL-like Lipase/Acylhydrolase family protein


Theoretical massNumber of molelcules
Total (without water)82,6132
Polymers82,6132
Non-polymers00
Water7,134396
1
A: GDSL-like Lipase/Acylhydrolase family protein


Theoretical massNumber of molelcules
Total (without water)41,3071
Polymers41,3071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GDSL-like Lipase/Acylhydrolase family protein


Theoretical massNumber of molelcules
Total (without water)41,3071
Polymers41,3071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.188, 79.069, 123.907
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GDSL-like Lipase/Acylhydrolase family protein


Mass: 41306.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: Neisseria meningitidis, NM4119_1198 / Plasmid: PGEX 4TI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: L5SU74
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Hepes pH 7.5 10-40% Peg 10000 , VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.334→40.41 Å / Num. obs: 2673 / % possible obs: 88.48 % / Observed criterion σ(F): 2.51 / Observed criterion σ(I): 2.51
Reflection shellResolution: 2.334→2.417 Å / % possible all: 98.13

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.334→40.41 Å / SU ML: 0.32 / σ(F): 1.39 / Phase error: 24.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2639 1516 5.01 %
Rwork0.1735 --
obs0.1779 -98.13 %
all-30271 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.334→40.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5310 0 0 396 5706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085433
X-RAY DIFFRACTIONf_angle_d1.2397369
X-RAY DIFFRACTIONf_dihedral_angle_d15.5521943
X-RAY DIFFRACTIONf_chiral_restr0.08806
X-RAY DIFFRACTIONf_plane_restr0.004962
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3338-2.40910.3321210.22822285X-RAY DIFFRACTION88
2.4091-2.49520.29471360.20872593X-RAY DIFFRACTION99
2.4952-2.59510.30591360.19222584X-RAY DIFFRACTION99
2.5951-2.71310.27041370.18262602X-RAY DIFFRACTION99
2.7131-2.85620.30921370.19142598X-RAY DIFFRACTION99
2.8562-3.0350.28761380.19352625X-RAY DIFFRACTION99
3.035-3.26930.27151400.17632644X-RAY DIFFRACTION99
3.2693-3.59810.26591390.16132641X-RAY DIFFRACTION99
3.5981-4.11830.25341400.152661X-RAY DIFFRACTION99
4.1183-5.18690.21531420.14542693X-RAY DIFFRACTION100
5.1869-40.41590.23761500.17662827X-RAY DIFFRACTION100

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