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- PDB-1tzp: MEPA, inactive form without ZN in P21 -

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Basic information

Entry
Database: PDB / ID: 1tzp
TitleMEPA, inactive form without ZN in P21
ComponentsPenicillin-insensitive murein endopeptidase
KeywordsHYDROLASE / LAS enzyme / metallopeptidase / peptidoglycan hydrolase
Function / homology
Function and homology information


peptidoglycan metabolic process / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / peptidoglycan biosynthetic process / metalloendopeptidase activity / peptidase activity / outer membrane-bounded periplasmic space / endopeptidase activity / response to xenobiotic stimulus / serine-type endopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase M74, penicillin-insensitive murein endopeptidase / Penicillin-insensitive murein endopeptidase / Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-BUTANEDIOL / Penicillin-insensitive murein endopeptidase / Penicillin-insensitive murein endopeptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMarcyjaniak, M. / Odintsov, S.G. / Sabala, I. / Bochtler, M.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Peptidoglycan amidase MepA is a LAS metallopeptidase
Authors: Marcyjaniak, M. / Odintsov, S.G. / Sabala, I. / Bochtler, M.
#1: Journal: Protein Sci. / Year: 2004
Title: Similar active sites in lysostaphins and D-Ala-D-Ala metallopeptidases
Authors: Bochtler, M. / Odintsov, S.G. / Marcyjaniak, M. / Sabala, I.
#2: Journal: J.Mol.Biol. / Year: 2004
Title: Latent LytM at 1.3A resolution
Authors: Odintsov, S.G. / Sabala, I. / Marcyjaniak, M. / Bochtler, M.
History
DepositionJul 11, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Penicillin-insensitive murein endopeptidase
B: Penicillin-insensitive murein endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,61812
Polymers56,6632
Non-polymers95510
Water10,016556
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.949, 115.143, 49.154
Angle α, β, γ (deg.)90.00, 94.08, 90.00
Int Tables number4
Space group name H-MP1211
DetailsDimer in three different crystal forms.lution not characterized

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Components

#1: Protein Penicillin-insensitive murein endopeptidase / D-alanyl-D-alanine-endopeptidase / DD-endopeptidase


Mass: 28331.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mepA / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P14007, UniProt: P0C0T5*PLUS, EC: 3.4.99.-
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: ammonium sulfate, MES, PEG monomethyl ether 5000, 1,4-butanediol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 26, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. obs: 91010 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 0.036 / Net I/σ(I): 10
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.129 / Mean I/σ(I) obs: 5.5 / Num. unique all: 13722 / Rsym value: 0.129 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A partial model of MEPA in a different crystal form

Resolution: 1.4→19.73 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.949 / SU B: 0.957 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.067 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2061 4528 5 %RANDOM
Rwork0.18334 ---
all0.18447 86482 --
obs0.18447 86482 91.11 %-
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: 13.402 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20.17 Å2
2--0.33 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3728 0 51 560 4339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0213866
X-RAY DIFFRACTIONr_bond_other_d0.0020.023452
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.9585254
X-RAY DIFFRACTIONr_angle_other_deg0.84138047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7715473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0890.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024251
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02759
X-RAY DIFFRACTIONr_nbd_refined0.2190.2779
X-RAY DIFFRACTIONr_nbd_other0.2480.23940
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.22013
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2341
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.237
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8221.52378
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4823836
X-RAY DIFFRACTIONr_scbond_it2.10431488
X-RAY DIFFRACTIONr_scangle_it3.3114.51418
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.244 320
Rwork0.205 6607

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