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- PDB-2pic: E. coli lytic transglycosylase MltA-D308A in apo-2 form -

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Basic information

Entry
Database: PDB / ID: 2pic
TitleE. coli lytic transglycosylase MltA-D308A in apo-2 form
ComponentsMembrane-bound lytic murein transglycosylase A
KeywordsHYDROLASE / double-psi beta-barrel / lytic transglycosylase / active site mutant
Function / homology
Function and homology information


: / peptidoglycan lytic transglycosylase activity / peptidoglycan metabolic process / peptidoglycan turnover / hydrolase activity, hydrolyzing O-glycosyl compounds / peptidoglycan catabolic process / cell outer membrane / cell wall organization / outer membrane-bounded periplasmic space
Similarity search - Function
Barwin-like endoglucanases / Lytic transglycosylase MltA, domain B / Membrane-bound lytic murein transglycosylase A / MltA specific insert domain / MltA specific insert domain / 3D domain / 3D domain / RlpA-like domain / RlpA-like domain superfamily / Ribosomal Protein L25; Chain P ...Barwin-like endoglucanases / Lytic transglycosylase MltA, domain B / Membrane-bound lytic murein transglycosylase A / MltA specific insert domain / MltA specific insert domain / 3D domain / 3D domain / RlpA-like domain / RlpA-like domain superfamily / Ribosomal Protein L25; Chain P / Barwin-like endoglucanases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Membrane-bound lytic murein transglycosylase A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
Authorsvan Straaten, K.E. / Dijkstra, B.W. / Thunnissen, A.M.W.H.
Citation
Journal: J.Biol.Chem. / Year: 2007
Title: Structure of Escherichia coli Lytic transglycosylase MltA with bound chitohexaose: implications for peptidoglycan binding and cleavage
Authors: van Straaten, K.E. / Barends, T.R. / Dijkstra, B.W. / Thunnissen, A.M.W.H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Escherichia coli MltA: MAD phasing and refinement of a tetartohedrally twinned protein crystal structure
Authors: Barends, T.R.M. / de Jong, R.M. / van Straaten, K.E. / Thunnissen, A.M.W.H. / Dijkstra, B.W.
#2: Journal: J.Mol.Biol. / Year: 2005
Title: Crystal structure of MltA from Escherichia coli reveals a unique lytic transglycosylase fold
Authors: van Straaten, K.E. / Dijkstra, B.W. / Vollmer, W. / Thunnissen, A.M.W.H.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Purification, crystallization and preliminary X-ray analysis of the lytic transglycosylase MltA from Escherichia coli
Authors: van Straaten, K.E. / Dijkstra, B.W. / Thunnissen, A.M.W.H.
History
DepositionApr 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Membrane-bound lytic murein transglycosylase A


Theoretical massNumber of molelcules
Total (without water)38,2071
Polymers38,2071
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.9, 80.9, 130.3
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-412-

HOH

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Components

#1: Protein Membrane-bound lytic murein transglycosylase A / E.C.3.2.1.- / Murein hydrolase A / Mlt38


Mass: 38206.680 Da / Num. of mol.: 1 / Mutation: D308A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: mltA, mlt / Plasmid: pMSS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P0A935, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 3.22 Å3/Da / Density % sol: 61.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.25-0.35M NaCl, 10mM magnesium chloride, 100mM sodium acetate buffer, pH 4.2, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. all: 22884 / Num. obs: 22884 / % possible obs: 93.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.063 / Χ2: 1.046 / Net I/σ(I): 21.5
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.25-2.330.3415841.292166
2.33-2.420.27720091.067184.1
2.42-2.530.25223581.119198.1
2.53-2.670.18123451.068198
2.67-2.830.12723591.017198.3
2.83-3.050.08923970.996198.7
3.05-3.360.06424200.981198.8
3.36-3.850.05224021.053198.2
3.85-4.840.0424431.02198.9
4.84-300.03825670.989198.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.1.24refinement
PDB_EXTRACT2data extraction
ProDCdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AE0

2ae0


Resolution: 2.25→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.265 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.245 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1155 5.1 %RANDOM
Rwork0.203 ---
all0.206 22709 --
obs0.206 22709 94.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.472 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20.62 Å20 Å2
2--1.25 Å20 Å2
3----1.87 Å2
Refinement stepCycle: LAST / Resolution: 2.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2640 0 0 138 2778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0212711
X-RAY DIFFRACTIONr_angle_refined_deg1.1351.933670
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.3975335
X-RAY DIFFRACTIONr_chiral_restr0.1050.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.022163
X-RAY DIFFRACTIONr_nbd_refined0.190.31116
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.549
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.327
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0620.53
X-RAY DIFFRACTIONr_mcbond_it3.2781.51663
X-RAY DIFFRACTIONr_mcangle_it5.0322655
X-RAY DIFFRACTIONr_scbond_it7.32231048
X-RAY DIFFRACTIONr_scangle_it10.0654.51015
LS refinement shellResolution: 2.25→2.273 Å / Total num. of bins used: 50
RfactorNum. reflection
Rfree0.44 23
Rwork0.325 407
obs-430

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