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- PDB-3d2y: Complex of the N-acetylmuramyl-L-alanine amidase AmiD from E.coli... -

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Basic information

Entry
Database: PDB / ID: 3d2y
TitleComplex of the N-acetylmuramyl-L-alanine amidase AmiD from E.coli with the substrate anhydro-N-acetylmuramic acid-L-Ala-D-gamma-Glu-L-Lys
Components
  • Anhydro-N-acetylmuramic acid-L-Ala-D-gamma-Glu-L-Lys
  • 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 / PGBD-like 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 (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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: Advisory / Database references ...Advisory / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetylmuramoyl-L-alanine amidase amiD
B: Anhydro-N-acetylmuramic acid-L-Ala-D-gamma-Glu-L-Lys
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1654
Polymers29,9812
Non-polymers1842
Water5,549308
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: N-acetylmuramoyl-L-alanine amidase amiD
B: Anhydro-N-acetylmuramic acid-L-Ala-D-gamma-Glu-L-Lys
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)60,3308
Polymers59,9624
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area6370 Å2
ΔGint-3 kcal/mol
Surface area22880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.274, 88.274, 181.834
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-329-

HOH

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 (E. coli) / 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 Anhydro-N-acetylmuramic acid-L-Ala-D-gamma-Glu-L-Lys


Mass: 604.626 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 3.41 Å3/Da / Density % sol: 63.94 %
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: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97885 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97885 Å / Relative weight: 1
ReflectionResolution: 1.75→47.5 Å / Num. obs: 42426 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 28.6
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.825 / Mean I/σ(I) obs: 2.2 / Num. unique all: 5643 / % possible all: 92.7

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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: 1.75→44.15 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.354 / SU ML: 0.091 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25326 2136 5 %RANDOM
Rwork0.2069 ---
obs0.20919 40210 98.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.923 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0.13 Å20 Å2
2---0.26 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.75→44.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 0 12 308 2418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222198
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.9673000
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5825266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.923.704108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.66915350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6631518
X-RAY DIFFRACTIONr_chiral_restr0.1110.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021709
X-RAY DIFFRACTIONr_nbd_refined0.1960.21033
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21464
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2216
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.228
X-RAY DIFFRACTIONr_mcbond_it2.50921366
X-RAY DIFFRACTIONr_mcangle_it3.19732137
X-RAY DIFFRACTIONr_scbond_it2.7992962
X-RAY DIFFRACTIONr_scangle_it3.9243858
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 169 -
Rwork0.283 2620 -
obs-2186 89.02 %
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)
123.01253.78070.445316.2316-6.6932.9413-1.0101-0.90690.3139-0.0810.2557-1.0070.6546-0.88560.75440.17550.2044-0.04820.0834-0.19590.158239.95413.92664.299
20.47180.40560.76370.48591.02212.21030.03890.0549-0.08830.08640.1163-0.20490.08080.2517-0.15520.01480.057-0.04280.075-0.0420.002736.21435.83784.369
31.7369-0.05631.38950.1626-0.2061.30470.0320.0688-0.03060.00540.0001-0.01260.06240.1134-0.0320.01710.0329-0.03450.0511-0.026-0.003134.90139.33686.843
437.16620.9934-23.616552.562126.915530.13031.0823-0.40012.25171.55-1.22731.6493-0.6493-1.38310.1450.17790.2256-0.03710.0839-0.19220.154427.14457.295103.599
51.7437-0.5612-0.18011.18891.22673.1218-0.07990.0427-0.018-0.04230.0447-0.162-0.24260.17160.0352-0.01940.0043-0.05210.0609-0.02030.005242.99448.39687.982
61.0927-0.59760.35890.4999-0.18871.4781-0.19140.05240.19830.06930.0337-0.0969-0.27610.18050.15770.0662-0.0397-0.09670.0182-0.0020.033632.04157.94181.678
71.9767-0.10710.34041.2552-0.61592.0199-0.17-0.07840.07980.08220.11150.1086-0.2191-0.13810.05850.06930.0594-0.05850.0064-0.0117-0.008619.17357.5983.23
81.7769-1.0616-0.16651.57450.18142.7197-0.15860.16080.31610.0193-0.1185-0.1628-0.5816-0.04490.2770.08620.0051-0.1235-0.05080.02720.030626.89962.5779.582
911.44482.85927.65234.90665.771616.20910.0507-0.59370.1170.5198-0.14340.07380.2098-0.39690.09270.06640.026-0.01250.0830.01720.005325.32839.05692.67
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 136 - 13
2X-RAY DIFFRACTION2AA14 - 6514 - 65
3X-RAY DIFFRACTION3AA66 - 10866 - 108
4X-RAY DIFFRACTION4AA109 - 118109 - 118
5X-RAY DIFFRACTION5AA119 - 140119 - 140
6X-RAY DIFFRACTION6AA141 - 198141 - 198
7X-RAY DIFFRACTION7AA199 - 235199 - 235
8X-RAY DIFFRACTION8AA236 - 261236 - 261
9X-RAY DIFFRACTION9BB1 - 41 - 4

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