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- PDB-4k7j: Peptidoglycan O-acetylesterase in action, 5 min -

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Basic information

Entry
Database: PDB / ID: 4k7j
TitlePeptidoglycan O-acetylesterase in action, 5 min
ComponentsGDSL-like Lipase/Acylhydrolase family protein
KeywordsHYDROLASE / alpha/Beta fold / peptidoglycan hydrolase
Function / homology
Function and homology information


Jelly Rolls - #1360 / SGNH hydrolase / Jelly Rolls / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.968 Å
AuthorsWilliams, A.H. / Gomperts 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 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Mar 26, 2025Group: 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6538
Polymers81,5822
Non-polymers1,0716
Water8,287460
1
A: GDSL-like Lipase/Acylhydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3264
Polymers40,7911
Non-polymers5363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GDSL-like Lipase/Acylhydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3264
Polymers40,7911
Non-polymers5363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.137, 79.982, 122.548
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: 40790.789 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: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / 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

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.61 %
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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.968→48.641 Å / Num. all: 49265 / % possible obs: 99.34 % / Observed criterion σ(F): 1.96 / Observed criterion σ(I): 1.96
Reflection shellResolution: 1.968→2.039 Å / % possible all: 99.34

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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: MOLECULAR REPLACEMENT / Resolution: 1.968→48.641 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 21.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2247 4958 10.07 %RANDOM
Rwork0.1665 ---
all0.1665 49265 --
obs0.1722 49259 99.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.968→48.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5314 0 67 460 5841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075543
X-RAY DIFFRACTIONf_angle_d1.1437519
X-RAY DIFFRACTIONf_dihedral_angle_d14.3592014
X-RAY DIFFRACTIONf_chiral_restr0.078811
X-RAY DIFFRACTIONf_plane_restr0.004974
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9683-1.99070.32611390.2581364X-RAY DIFFRACTION94
1.9907-2.01410.33491860.24871472X-RAY DIFFRACTION100
2.0141-2.03870.27551540.23141442X-RAY DIFFRACTION100
2.0387-2.06450.2661760.21761452X-RAY DIFFRACTION99
2.0645-2.09170.30031800.21771444X-RAY DIFFRACTION100
2.0917-2.12030.26891700.20361453X-RAY DIFFRACTION100
2.1203-2.15060.28531690.20021443X-RAY DIFFRACTION100
2.1506-2.18270.25921580.19181475X-RAY DIFFRACTION100
2.1827-2.21680.26771780.18851468X-RAY DIFFRACTION100
2.2168-2.25320.27141630.18021450X-RAY DIFFRACTION99
2.2532-2.2920.26611690.17881444X-RAY DIFFRACTION99
2.292-2.33370.24961770.18681458X-RAY DIFFRACTION100
2.3337-2.37860.27261570.18241469X-RAY DIFFRACTION100
2.3786-2.42710.25811640.17761510X-RAY DIFFRACTION100
2.4271-2.47990.25481680.16781437X-RAY DIFFRACTION100
2.4799-2.53760.25731670.17941479X-RAY DIFFRACTION100
2.5376-2.6010.23771610.16431476X-RAY DIFFRACTION100
2.601-2.67140.23651510.16471493X-RAY DIFFRACTION100
2.6714-2.750.25271710.16551456X-RAY DIFFRACTION100
2.75-2.83870.24631550.16411482X-RAY DIFFRACTION99
2.8387-2.94020.1971650.17051487X-RAY DIFFRACTION100
2.9402-3.05790.20731600.16631495X-RAY DIFFRACTION99
3.0579-3.1970.21191630.16011482X-RAY DIFFRACTION99
3.197-3.36550.21481500.16291498X-RAY DIFFRACTION100
3.3655-3.57630.22771470.15041511X-RAY DIFFRACTION100
3.5763-3.85230.18971580.14641489X-RAY DIFFRACTION98
3.8523-4.23980.19211660.13981507X-RAY DIFFRACTION100
4.2398-4.85280.1791620.13671526X-RAY DIFFRACTION100
4.8528-6.11220.18531790.15451532X-RAY DIFFRACTION99
6.1122-48.65560.19871950.1671607X-RAY DIFFRACTION99

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