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- PDB-2wkx: Crystal structure of the native E. coli zinc amidase AmiD -

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Basic information

Entry
Database: PDB / ID: 2wkx
TitleCrystal structure of the native E. coli zinc amidase AmiD
ComponentsN-ACETYLMURAMOYL-L-ALANINE AMIDASE AMID
KeywordsHYDROLASE / OUTER MEMBRANE / CELL WALL BIOGENESIS/DEGRADATION / CELL MEMBRANE / METAL-BINDING
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: 1.8 Å
AuthorsPetrella, S. / Kerff, F. / Herman, R. / Genereux, C. / Pennartz, A. / Sauvage, E. / 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
DepositionJun 18, 2009Deposition site: PDBE / Processing site: PDBE
SupersessionJan 12, 2010ID: 2BGX
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8818
Polymers29,3761
Non-polymers5057
Water4,306239
1
A: N-ACETYLMURAMOYL-L-ALANINE AMIDASE AMID
hetero molecules

A: N-ACETYLMURAMOYL-L-ALANINE AMIDASE AMID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,76216
Polymers58,7522
Non-polymers1,00914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area8320 Å2
ΔGint-122.96 kcal/mol
Surface area22670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.990, 88.990, 183.923
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein N-ACETYLMURAMOYL-L-ALANINE AMIDASE AMID


Mass: 29376.240 Da / Num. of mol.: 1 / Fragment: RESIDUES 18-276
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 MG1655 / Plasmid: PBAD/MYC-HISA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): LMG194
References: UniProt: P75820, N-acetylmuramoyl-L-alanine amidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


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


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


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE N-TERMINAL CYSTEINE OF THE PROCESSED PROTEIN WAS REPLACED BY A GLYCINE. A METHIONINE WAS ADDED ...THE N-TERMINAL CYSTEINE OF THE PROCESSED PROTEIN WAS REPLACED BY A GLYCINE. A METHIONINE WAS ADDED AT THE N- TERMINUS.

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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: 3.19 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 4 / Details: 1M LICL, 10 % PEG 6K, 0.1M ZNCL2, PH 4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9791
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 6, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.8→21.38 Å / Num. obs: 41725 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.7 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BH7

2bh7


Resolution: 1.8→21.23 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.842 / SU ML: 0.049 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18367 4027 10 %RANDOM
Rwork0.16077 ---
obs0.16302 36115 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.313 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.27 Å20 Å2
2--0.54 Å20 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.8→21.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 27 239 2322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222168
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.962958
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6595268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76123.889108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47115346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7951517
X-RAY DIFFRACTIONr_chiral_restr0.0910.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021700
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.180.2997
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21468
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2139
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1130.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.79721362
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.3832116
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1862946
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3833836
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: 1.8→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 219 -
Rwork0.25 2022 -
obs--76.3 %
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)
118.44851.5596-1.040516.6279-3.35484.0129-0.10570.1892-0.0972-0.1977-0.0611-1.32130.90740.75720.1668-0.08510.1965-0.10410.1608-0.12820.061640.866714.732164.3252
20.46640.41780.74950.84331.30932.0721-0.02290.0702-0.1030.1250.1498-0.17890.11530.2611-0.12690.04070.0394-0.04420.072-0.04430.045336.773136.579385.3468
31.3281-0.04730.80551.0840.19121.436-0.02470.0754-0.07860.05680.1002-0.02730.1550.1527-0.07550.04180.0236-0.03710.0435-0.03250.017734.146540.299787.37
410.66520.5112-7.808517.62-1.299427.0776-0.6067-0.51250.30361.94561.17771.1687-2.0703-1.5479-0.57110.34730.4030.04710.13570.00130.024827.541158.3995104.3375
51.4403-0.44720.2121.07110.28681.5301-0.10780.06990.0360.02240.0963-0.0818-0.10640.16570.01150.0269-0.001-0.04950.0373-0.020.013136.434750.32386.5016
61.1121-0.40860.21111.3168-0.12851.12-0.07650.02990.117-0.05510.0404-0.0303-0.2760.07780.03620.1-0.0246-0.07390.0030.02130.009427.698164.142478.2674
712.55283.15634.931518.783618.035940.99050.07050.0485-0.83570.2894-0.07850.61160.5832-0.89350.008-0.0840.0667-0.02340.05160.05120.102110.574255.744485.7095
814.83494.59131.21756.2511-3.4143.2848-0.0532-0.3010.40160.14120.1330.3359-0.2559-0.2117-0.07980.0840.0516-0.05440.0116-0.01320.01920.00459.082587.7619
91.2155-0.65010.16221.16140.32472.4669-0.0960.04880.15940.0320.0189-0.031-0.36530.0620.0770.0962-0.0046-0.0853-0.01050.02050.030627.563263.394681.3959
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 13
2X-RAY DIFFRACTION2A14 - 66
3X-RAY DIFFRACTION3A67 - 108
4X-RAY DIFFRACTION4A109 - 118
5X-RAY DIFFRACTION5A119 - 170
6X-RAY DIFFRACTION6A171 - 214
7X-RAY DIFFRACTION7A215 - 221
8X-RAY DIFFRACTION8A222 - 231
9X-RAY DIFFRACTION9A232 - 261

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