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- PDB-2gae: Crystal structure of MltA from E. coli -

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Basic information

Entry
Database: PDB / ID: 2gae
TitleCrystal structure of MltA from E. coli
ComponentsMembrane-bound lytic murein transglycosylase A
KeywordsHYDROLASE / BETA BARREL
Function / homology
Function and homology information


: / lytic transglycosylase activity / peptidoglycan turnover / peptidoglycan metabolic process / 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 / SAD / Resolution: 2.5 Å
AuthorsPowell, A.J. / Liu, Z.J. / Nicholas, R.A. / Davies, C.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structures of the Lytic Transglycosylase MltA from N.gonorrhoeae and E.coli: Insights into Interdomain Movements and Substrate Binding.
Authors: Powell, A.J. / Liu, Z.J. / Nicholas, R.A. / Davies, C.
History
DepositionMar 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)38,2741
Polymers38,2741
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.880, 103.880, 110.560
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Membrane-bound lytic murein transglycosylase A / Murein hydrolase A / Mlt38


Mass: 38273.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mltA, mlt / Plasmid: pMAL-c2KV / Production host: Escherichia coli (E. coli) / 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.: 33 / 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: 4.5 Å3/Da / Density % sol: 72.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 10 % PEG 8000, 100 mM sodium acetate, 10 mM magnesium chloride & 360 mM sodium chloride, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 29, 2004 / Details: Osmic mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 23998 / Num. obs: 23998 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.65 % / Biso Wilson estimate: 60.8 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.98 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 3.4 / Num. unique all: 4351 / % possible all: 93.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
d*TREKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.881 / SU B: 20.342 / SU ML: 0.214 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.303 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.31 1213 5.1 %RANDOM
Rwork0.253 ---
all0.256 23998 --
obs0.256 23998 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.355 Å2
Baniso -1Baniso -2Baniso -3
1-3.01 Å21.51 Å20 Å2
2--3.01 Å20 Å2
3----4.52 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2625 0 0 33 2658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222693
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.9363647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9915332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22123.643140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.30115421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5891521
X-RAY DIFFRACTIONr_chiral_restr0.0790.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022151
X-RAY DIFFRACTIONr_nbd_refined0.2130.21098
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21804
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.282
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.22
X-RAY DIFFRACTIONr_mcbond_it0.5571.51688
X-RAY DIFFRACTIONr_mcangle_it0.9822630
X-RAY DIFFRACTIONr_scbond_it1.14531161
X-RAY DIFFRACTIONr_scangle_it1.8464.51017
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 74 -
Rwork0.349 1639 -
obs-2713 97.5 %
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)
11.18160.31680.33961.18341.18422.42750.1052-0.17820.0012-0.0414-0.0824-0.04530.0811-0.3388-0.0229-0.0109-0.037-0.01590.04040.0155-0.0744-0.544857.24526.9292
23.6501-0.18310.73150.6109-0.1552.520.26280.2757-0.3721-0.0415-0.08250.05510.25820.0989-0.18030.04560.0271-0.1297-0.0801-0.04040.016510.258436.3846-14.6398
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA24 - 1235 - 104
2X-RAY DIFFRACTION1AA262 - 356243 - 337
3X-RAY DIFFRACTION2AA124 - 261105 - 242

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