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- PDB-4bh5: LytM domain of EnvC, an activator of cell wall amidases in Escher... -

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Basic information

Entry
Database: PDB / ID: 4bh5
TitleLytM domain of EnvC, an activator of cell wall amidases in Escherichia coli
ComponentsMUREIN HYDROLASE ACTIVATOR ENVC
KeywordsCELL CYCLE / AMIDASE ACTIVATOR / AUTOLYSIN / CYTOKINESIS / MORPHOGENESIS / SACCULUS / PEPTIDOGLYCAN
Function / homology
Function and homology information


peptidoglycan-based cell wall biogenesis / septum digestion after cytokinesis / cell division site / response to radiation / metalloendopeptidase activity / outer membrane-bounded periplasmic space / periplasmic space / hydrolase activity / response to xenobiotic stimulus / plasma membrane
Similarity search - Function
Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / : / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / : / Murein hydrolase activator EnvC
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsMorlot, C. / Peters, N.T. / Yang, D.C. / Uehara, T. / Vernet, T. / Bernhardt, T.G.
CitationJournal: Mol.Microbiol. / Year: 2013
Title: Structure-Function Analysis of the Lytm Domain of Envc, an Activator of Cell Wall Remodeling at the Escherichia Coli Division Site.
Authors: Peters, N.T. / Morlot, C. / Yang, D.C. / Uehara, T. / Vernet, T. / Bernhardt, T.G.
History
DepositionMar 29, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Oct 16, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / reflns / reflns_shell
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MUREIN HYDROLASE ACTIVATOR ENVC
B: MUREIN HYDROLASE ACTIVATOR ENVC
C: MUREIN HYDROLASE ACTIVATOR ENVC
D: MUREIN HYDROLASE ACTIVATOR ENVC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,29334
Polymers61,0094
Non-polymers3,28430
Water7,008389
1
A: MUREIN HYDROLASE ACTIVATOR ENVC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7956
Polymers15,2521
Non-polymers5435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MUREIN HYDROLASE ACTIVATOR ENVC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,30310
Polymers15,2521
Non-polymers1,0519
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: MUREIN HYDROLASE ACTIVATOR ENVC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,18010
Polymers15,2521
Non-polymers9289
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: MUREIN HYDROLASE ACTIVATOR ENVC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0148
Polymers15,2521
Non-polymers7627
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.404, 57.404, 129.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
MUREIN HYDROLASE ACTIVATOR ENVC / SEPTAL RING FACTOR


Mass: 15252.239 Da / Num. of mol.: 4 / Fragment: LYTM DOMAIN, RESIDUES 278-419
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PTB104 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37690

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Non-polymers , 5 types, 419 molecules

#2: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 2.02 Å3/Da / Density % sol: 39.2 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.9 / Details: 0.2 M SODIUM IODIDE, 17% PEG 3350, PH 6.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.56→46.4 Å / Num. obs: 64864 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 2.89 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 15.9
Reflection shellResolution: 1.56→1.66 Å / Redundancy: 2.19 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 2.8 / % possible all: 73

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NE8

3ne8


Resolution: 1.57→46.4 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.721 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20724 6369 9.9 %RANDOM
Rwork0.16641 ---
obs0.17044 57816 96.39 %-
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: 14.897 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å2-0.21 Å20 Å2
2---0.42 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.57→46.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3936 0 40 389 4365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224127
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.9535599
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2865542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.42822.66188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87515658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1171543
X-RAY DIFFRACTIONr_chiral_restr0.1180.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213239
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.57→1.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 367 -
Rwork0.266 3228 -
obs--73.02 %

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