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- PDB-4xp8: Structure of EtgA D60N mutant -

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Basic information

Entry
Database: PDB / ID: 4xp8
TitleStructure of EtgA D60N mutant
ComponentsEtgA protein
KeywordsHYDROLASE / peptidoglycan hydrolase
Function / homologyTransglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysozyme-like domain superfamily / EtgA protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.03 Å
AuthorsBurkinshaw, B.J. / Worrall, L.J. / Strynadka, N.C.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Analysis of a Specialized Type III Secretion System Peptidoglycan-cleaving Enzyme.
Authors: Burkinshaw, B.J. / Deng, W. / Lameignere, E. / Wasney, G.A. / Zhu, H. / Worrall, L.J. / Finlay, B.B. / Strynadka, N.C.
History
DepositionJan 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Apr 29, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EtgA protein


Theoretical massNumber of molelcules
Total (without water)9,8861
Polymers9,8861
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.400, 31.400, 149.530
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein EtgA protein


Mass: 9886.001 Da / Num. of mol.: 1 / Fragment: UNP residues 19-104 / Mutation: D60N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: etgA / Production host: Escherichia coli (E. coli) / References: UniProt: C7BUG6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.15 Å3/Da / Density % sol: 42.86 % / Description: diamond-shaped
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 0.1M imidazole, pH 7.3, 20% 2-propanol

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9795, 0.9797, 0.9611
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97971
30.96111
ReflectionResolution: 2.03→29.9 Å / Num. obs: 6064 / % possible obs: 99 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.046 / Net I/σ(I): 14 / Num. measured all: 41538
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.03-2.097.30.7583.235104810.8560.29899.5
8.85-29.94.80.04725.94771000.9970.02395.2

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Processing

Software
NameVersionClassification
Aimless0.2.14data scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
SHARPphasing
RefinementResolution: 2.03→29.9 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.938 / SU B: 11.174 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 607 9.8 %RANDOM
Rwork0.2075 5584 --
obs0.2113 6064 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.91 Å2 / Biso mean: 39.846 Å2 / Biso min: 21.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20.31 Å20 Å2
2--0.63 Å2-0 Å2
3----2.04 Å2
Refinement stepCycle: final / Resolution: 2.03→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms685 0 0 17 702
Biso mean---41.45 -
Num. residues----88
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02700
X-RAY DIFFRACTIONr_bond_other_d0.0010.02688
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.967946
X-RAY DIFFRACTIONr_angle_other_deg0.9463.0041585
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.0215.27890
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.8527.24129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.60815128
X-RAY DIFFRACTIONr_chiral_restr0.0920.2109
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02807
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02151
X-RAY DIFFRACTIONr_mcbond_it2.2942.53353
X-RAY DIFFRACTIONr_mcbond_other2.272.523352
X-RAY DIFFRACTIONr_mcangle_it3.1823.778440
LS refinement shellResolution: 2.03→2.062 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 34 -
Rwork0.255 404 -
all-438 -
obs--99.55 %
Refinement TLS params.Method: refined / Origin x: 25.045 Å / Origin y: 24.062 Å / Origin z: -9.554 Å
111213212223313233
T0.0346 Å2-0.0093 Å2-0.0059 Å2-0.0699 Å2-0.013 Å2--0.0043 Å2
L2.3654 °2-0.584 °20.2371 °2-3.3942 °2-0.4856 °2--5.6428 °2
S0.0821 Å °0.245 Å °-0.0724 Å °-0.2077 Å °-0.0296 Å °0.0465 Å °0.2403 Å °-0.0931 Å °-0.0525 Å °

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