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- PDB-2bh7: Crystal structure of a SeMet derivative of AmiD at 2.2 angstroms -

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Basic information

Entry
Database: PDB / ID: 2bh7
TitleCrystal structure of a SeMet derivative of AmiD at 2.2 angstroms
ComponentsN-ACETYLMURAMOYL-L-ALANINE AMIDASE
KeywordsHYDROLASE / ZINC AMIDASE / PGRP / T7 LYSOZYME / AMPD
Function / homology
Function and homology information


N-acetyl-anhydromuramoyl-L-alanine amidase activity / N-acetylmuramoyl-L-alanine amidase / peptidoglycan turnover / N-acetylmuramoyl-L-alanine amidase activity / outer membrane / peptidoglycan catabolic process / cell wall organization / cell outer membrane / zinc ion binding
Similarity search - Function
Rhinovirus 14, subunit 4 - #150 / Rhinovirus 14, subunit 4 / 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 ...Rhinovirus 14, subunit 4 - #150 / Rhinovirus 14, subunit 4 / 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 / Other non-globular / Special / 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 / SAD / Resolution: 2.2 Å
AuthorsPetrella, S. / Herman, R. / Sauvage, E. / Genereux, C. / Pennartz, A. / 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
DepositionJan 7, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-ACETYLMURAMOYL-L-ALANINE AMIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2068
Polymers29,5641
Non-polymers6427
Water2,648147
1
A: N-ACETYLMURAMOYL-L-ALANINE AMIDASE
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)60,41116
Polymers59,1282
Non-polymers1,28414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area7830 Å2
ΔGint-246.4 kcal/mol
Surface area21900 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 /


Mass: 29563.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 MG1655
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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 1 TO 17 WERE REMOVED AND A METHIONINE AND A GLYCINE WERE ADDED AT THE BEGINNING OF THE PROTEIN

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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: 3.4 Å3/Da / Density % sol: 63 %
Crystal growpH: 4.6 / Details: 1M MGSO4 ACETATE PH 5.6

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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: 2.2→27.77 Å / Num. obs: 22663 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 48.3 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 57
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 23.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 8.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→27.77 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2131583.74 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.279 2167 9.9 %RANDOM
Rwork0.231 ---
obs0.231 21818 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.3704 Å2 / ksol: 0.388993 e/Å3
Displacement parametersBiso mean: 36.4 Å2
Baniso -1Baniso -2Baniso -3
1-5.06 Å24.48 Å20 Å2
2--5.06 Å20 Å2
3----10.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.2→27.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2029 0 31 147 2207
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.382
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it3.232.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 332 10.5 %
Rwork0.311 2838 -
obs--86.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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