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- PDB-3d2z: Complex of the N-acetylmuramyl-L-alanine amidase AmiD from E.coli... -

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Basic information

Entry
Database: PDB / ID: 3d2z
TitleComplex of the N-acetylmuramyl-L-alanine amidase AmiD from E.coli with the product L-Ala-D-gamma-Glu-L-Lys
Components
  • L-Ala-D-gamma-Glu-L-Lys peptide
  • N-acetylmuramoyl-L-alanine amidase amiD
KeywordsHYDROLASE / ZINC AMIDASE / PGRP / Peptidoglycan Recognizing Protein / AmpD / N-ACETYLMURAMYL-L-ALANINE AMIDASE / Cell wall biogenesis/degradation / Lipoprotein / Membrane / Metal-binding / Outer membrane / Palmitate
Function / homology
Function and homology information


N-acetyl-anhydromuramoyl-L-alanine amidase activity / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan turnover / outer membrane / peptidoglycan catabolic process / cell outer membrane / cell wall organization / zinc ion binding
Similarity search - Function
Muramoyl-pentapeptide Carboxypeptidase; domain 1 / PGBD-like superfamily/PGBD / : / PGBD superfamily / Lysozyme-like / Peptidoglycan recognition protein-like / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily ...Muramoyl-pentapeptide Carboxypeptidase; domain 1 / PGBD-like superfamily/PGBD / : / PGBD superfamily / Lysozyme-like / Peptidoglycan recognition protein-like / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / PGBD-like superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
N-acetylmuramoyl-L-alanine amidase AmiD
Similarity search - Component
Biological speciesEscherichia coli str. K12 substr. MG1655 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKerff, F. / Petrella, S. / Herman, R. / Sauvage, E. / Mercier, F. / Luxen, A. / Frere, J.M. / Joris, B. / Charlier, P.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Specific Structural Features of the N-Acetylmuramoyl-l-Alanine Amidase AmiD from Escherichia coli and Mechanistic Implications for Enzymes of This Family.
Authors: Kerff, F. / Petrella, S. / Mercier, F. / Sauvage, E. / Herman, R. / Pennartz, A. / Zervosen, A. / Luxen, A. / Frere, J.M. / Joris, B. / Charlier, P.
History
DepositionMay 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Database references / Derived calculations / Non-polymer description
Revision 1.3Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_validate_polymer_linkage / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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: N-acetylmuramoyl-L-alanine amidase amiD
B: L-Ala-D-gamma-Glu-L-Lys peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8905
Polymers29,7242
Non-polymers1663
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-70.8 kcal/mol
Surface area14310 Å2
MethodPISA
2
A: N-acetylmuramoyl-L-alanine amidase amiD
B: L-Ala-D-gamma-Glu-L-Lys peptide
hetero molecules

A: N-acetylmuramoyl-L-alanine amidase amiD
B: L-Ala-D-gamma-Glu-L-Lys peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,78010
Polymers59,4474
Non-polymers3336
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z+1/21
Buried area7020 Å2
ΔGint-171.6 kcal/mol
Surface area23400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.160, 89.160, 183.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe biological assembly is a monomer but the protein is found as a dimer in the crystal with a swapping of the N-terminus

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Components

#1: Protein N-acetylmuramoyl-L-alanine amidase amiD


Mass: 29376.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K12 substr. MG1655 (bacteria)
Strain: K-12 MG1655 / Gene: amiD, ybjR, b0867, JW0851 / Plasmid: pBAD/Myc-HisA / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194
References: UniProt: P75820, N-acetylmuramoyl-L-alanine amidase
#2: Protein/peptide L-Ala-D-gamma-Glu-L-Lys peptide


Mass: 347.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.54 Å3/Da / Density % sol: 65.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 1M LICL, 10 % PEG 6K, 0.1M ZNCL2, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 20, 2007
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→47.9 Å / Num. obs: 11312 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.4 % / Rmerge(I) obs: 0.263 / Net I/σ(I): 14.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 21 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 4.9 / Num. unique all: 1592 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BGX

2bgx
PDB Unreleased entry


Resolution: 2.8→47.9 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.859 / SU B: 13.913 / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.582 / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26469 551 4.9 %RANDOM
Rwork0.20211 ---
obs0.20526 10706 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.079 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.16 Å20 Å2
2--0.31 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2071 0 3 76 2150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222127
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.9542897
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3685256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41523.654104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.72315339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0081517
X-RAY DIFFRACTIONr_chiral_restr0.0870.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021668
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.2847
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21419
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.261
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0840.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.89421343
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53732095
X-RAY DIFFRACTIONr_scbond_it0.6472910
X-RAY DIFFRACTIONr_scangle_it1.0693802
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 41 -
Rwork0.305 775 -
obs-551 100 %

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