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- PDB-2pjj: E. coli lytic transglycosylase MltA-D308A in apo-1 form -

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Basic information

Entry
Database: PDB / ID: 2pjj
TitleE. coli lytic transglycosylase MltA-D308A in apo-1 form
ComponentsMembrane-bound lytic murein transglycosylase A
KeywordsHYDROLASE / double-psi beta-barrel / protein-sugar complex / lytic transglycosylase
Function / homology
Function and homology information


: / lytic transglycosylase activity / peptidoglycan turnover / hydrolase activity, hydrolyzing O-glycosyl compounds / peptidoglycan catabolic process / cell wall organization / cell outer membrane / 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: 2.46 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 16, 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
Water4,089227
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.9, 104.9, 109.9
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number152
Space group name H-MP3121

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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 / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 4.57 Å3/Da / Density % sol: 73.06 %
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: 2.46→30 Å / Num. all: 25918 / Num. obs: 25840 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Biso Wilson estimate: 46.3 Å2 / Rmerge(I) obs: 0.06 / Χ2: 1.085 / Net I/σ(I): 20.8
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.46-2.550.33525331.3651100
2.55-2.650.25225561.1931100
2.65-2.770.18525801.0631100
2.77-2.920.13425560.981100
2.92-3.10.09325600.9871100
3.1-3.340.06325721.0491100
3.34-3.670.0525731.077199.9
3.67-4.20.04226101.072199.9
4.2-5.290.03626131.045199.7
5.29-300.03626871.034198.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
ProDCdata collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2AE0

2ae0


Resolution: 2.46→14.94 Å / Rfactor Rfree error: 0.006 / FOM work R set: 0.849 / Data cutoff high absF: 1353221.875 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1321 5.1 %RANDOM
Rwork0.21 ---
all0.212 25670 --
obs0.212 25670 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.755 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 38.7 Å2
Baniso -1Baniso -2Baniso -3
1-7.85 Å25.4 Å20 Å2
2--7.85 Å20 Å2
3----15.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.46→14.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2634 0 0 227 2861
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.73
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.46-2.490.334520.274937989
2.49-2.530.312540.283907961
2.53-2.560.355450.269938983
2.56-2.60.282590.256902961
2.6-2.640.333490.259926975
2.64-2.680.253630.232914977
2.68-2.730.299410.243915956
2.73-2.780.234590.234932991
2.78-2.830.241460.222949995
2.83-2.890.242530.224901954
2.89-2.950.211570.223932989
2.95-3.020.246510.226926977
3.02-3.090.232450.213946991
3.09-3.180.231590.215933992
3.18-3.270.265400.233928968
3.27-3.370.24520.225946998
3.37-3.490.238520.217927979
3.49-3.630.263540.221929983
3.63-3.790.215540.2079511005
3.79-3.990.175470.196937984
3.99-4.240.217530.18940993
4.24-4.550.221460.164952998
4.55-50.158530.1669511004
5-5.690.203510.1959501001
5.69-7.040.257470.2139741021
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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