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- PDB-5m38: Structure of the TagL peptidoglycan binding domain from EAEC T6SS -

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Basic information

Entry
Database: PDB / ID: 5m38
TitleStructure of the TagL peptidoglycan binding domain from EAEC T6SS
ComponentsOmpA family protein
KeywordsSUGAR BINDING PROTEIN / T6SS TagL Peptidoglycan binding domain
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
OmpA-like domain / Outer membrane protein, bacterial / : / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Type VI secretion protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCambillau, C. / Nguyen, V.S. / Spinelli, S. / Cascales, E.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR- 14-CE14-0006-01 France
CitationJournal: To Be Published
Title: Structure of the TagL peptidoglycan binding domain from EAEC T6SS
Authors: Cambillau, C. / Nguyen, V.S. / Cascales, E.
History
DepositionOct 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: OmpA family protein
B: OmpA family protein
C: OmpA family protein


Theoretical massNumber of molelcules
Total (without water)45,2823
Polymers45,2823
Non-polymers00
Water1,62190
1
A: OmpA family protein


Theoretical massNumber of molelcules
Total (without water)15,0941
Polymers15,0941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: OmpA family protein


Theoretical massNumber of molelcules
Total (without water)15,0941
Polymers15,0941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: OmpA family protein


Theoretical massNumber of molelcules
Total (without water)15,0941
Polymers15,0941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)211.550, 211.550, 211.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132

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Components

#1: Protein OmpA family protein


Mass: 15093.977 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ACU81_04615 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0P7P0J8, UniProt: D3GUV9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 4.36 Å3/Da / Density % sol: 71.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: mixing protein solution (5 mg/ml) with 0.1 M imidazole pH 6.5, 1.2 M NaAc
PH range: 6.0 - 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.6→45.1 Å / Num. obs: 25065 / % possible obs: 99.8 % / Redundancy: 9 % / Biso Wilson estimate: 97.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Net I/σ(I): 18.5
Reflection shellResolution: 2.6→2.71 Å / Redundancy: 9.5 % / Mean I/σ(I) obs: 1.5 / CC1/2: 0.53 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TD5

3td5


Resolution: 2.6→45.1 Å / Cor.coef. Fo:Fc: 0.9333 / Cor.coef. Fo:Fc free: 0.9347 / SU R Cruickshank DPI: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.259 / SU Rfree Blow DPI: 0.202 / SU Rfree Cruickshank DPI: 0.199
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 1253 5 %RANDOM
Rwork0.2168 ---
obs0.2176 25063 99.92 %-
Displacement parametersBiso mean: 85.38 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.434 Å
Refinement stepCycle: 1 / Resolution: 2.6→45.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2543 0 0 90 2633
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012592HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.313533HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d872SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes60HARMONIC2
X-RAY DIFFRACTIONt_gen_planes383HARMONIC5
X-RAY DIFFRACTIONt_it2592HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion20.26
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion344SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2921SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.71 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.309 139 5.03 %
Rwork0.2705 2627 -
all0.2724 2766 -
obs--99.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4342-0.5292-0.60310.90350.09121.10710.0082-0.0016-0.00810.0224-0.0039-0.0004-0.08280.0192-0.00430.00620.0580.1016-0.06520.12940.0341-7.9898-4.9817-25.0073
20.667-0.0636-0.26341.89150.35421.4414-0.012-0.011-0.0078-0.0339-0.0089-0.0126-0.04110.02020.02090.08710.03460.1274-0.20740.10260.08319.5986-15.4023-48.1914
31.0875-1.7319-0.3041.1445-1.11350.6770.00690.0410.00740.02270.0099-0.0185-0.00160.0634-0.0168-0.00410.13520.1057-0.04490.1390.041327.9847-30.4935-61.7437
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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