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- PDB-2y28: crystal structure of Se-Met AmpD derivative -

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Basic information

Entry
Database: PDB / ID: 2y28
Titlecrystal structure of Se-Met AmpD derivative
Components1,6-ANHYDRO-N-ACETYLMURAMYL-L-ALANINE AMIDASE AMPD
KeywordsHYDROLASE / PEPTIDOGLYCAN AMIDASE / AMIDASE_2 FAMILY / ACTIVATION MECHANISM
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / cell wall organization / metal ion binding / cytoplasm
Similarity search - Function
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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD
Similarity search - Component
Biological speciesCITROBACTER FREUNDII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsCarrasco-Lopez, C. / Rojas-Altuve, A. / Zhang, W. / Hesek, D. / Lee, M. / Barbe, S. / Andre, I. / Silva-Martin, N. / Martinez-Ripoll, M. / Mobashery, S. / Hermoso, J.A.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal Structures of Bacterial Peptidoglycan Amidase Ampd and an Unprecedented Activation Mechanism.
Authors: Carrasco-Lopez, C. / Rojas-Altuve, A. / Zhang, W. / Hesek, D. / Lee, M. / Barbe, S. / Andre, I. / Ferrer, P. / Silva-Martin, N. / Castro, G.R. / Martinez-Ripoll, M. / Mobashery, S. / Hermoso, J.A.
History
DepositionDec 14, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2011Group: Database references
Revision 1.2Dec 28, 2011Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1,6-ANHYDRO-N-ACETYLMURAMYL-L-ALANINE AMIDASE AMPD
B: 1,6-ANHYDRO-N-ACETYLMURAMYL-L-ALANINE AMIDASE AMPD
C: 1,6-ANHYDRO-N-ACETYLMURAMYL-L-ALANINE AMIDASE AMPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2326
Polymers63,0363
Non-polymers1963
Water12,412689
1
A: 1,6-ANHYDRO-N-ACETYLMURAMYL-L-ALANINE AMIDASE AMPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0772
Polymers21,0121
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 1,6-ANHYDRO-N-ACETYLMURAMYL-L-ALANINE AMIDASE AMPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0772
Polymers21,0121
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 1,6-ANHYDRO-N-ACETYLMURAMYL-L-ALANINE AMIDASE AMPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0772
Polymers21,0121
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.693, 67.693, 92.681
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein 1,6-ANHYDRO-N-ACETYLMURAMYL-L-ALANINE AMIDASE AMPD / N-ACETYLMURAMOYL-L-ALANINE AMIDASE / AMPD


Mass: 21012.045 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: SE-MET DERIVATIVE / Source: (gene. exp.) CITROBACTER FREUNDII (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P82974, N-acetylmuramoyl-L-alanine amidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 689 / 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: 2 Å3/Da / Density % sol: 37 % / Description: NONE
Crystal growpH: 6 / Details: 0.1 M TRIS PH 6.0, 0.1 M LI2SO4, 28% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97856, 0.978910, 0.918400
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 15, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978561
20.978911
30.91841
ReflectionResolution: 1.8→58.62 Å / Num. obs: 42178 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 15.89 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 16
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.6 / % possible all: 76

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.8→58.624 Å / SU ML: 0.24 / σ(F): 2 / Phase error: 22.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2318 4252 10.18 %
Rwork0.178 --
obs0.1835 42178 95.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.206 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso mean: 17 Å2
Baniso -1Baniso -2Baniso -3
1-1.8278 Å20 Å20 Å2
2--1.8278 Å20 Å2
3----3.6555 Å2
Refinement stepCycle: LAST / Resolution: 1.8→58.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4224 0 3 689 4916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114376
X-RAY DIFFRACTIONf_angle_d1.0785990
X-RAY DIFFRACTIONf_dihedral_angle_d16.3731552
X-RAY DIFFRACTIONf_chiral_restr0.07633
X-RAY DIFFRACTIONf_plane_restr0.005798
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.86440.26633410.20162908X-RAY DIFFRACTION74
1.8644-1.9390.24233680.19283460X-RAY DIFFRACTION86
1.939-2.02730.2534260.18433848X-RAY DIFFRACTION98
2.0273-2.13410.22894510.16923965X-RAY DIFFRACTION100
2.1341-2.26790.23094340.16633984X-RAY DIFFRACTION100
2.2679-2.4430.23574490.16823925X-RAY DIFFRACTION100
2.443-2.68880.2394390.1683997X-RAY DIFFRACTION100
2.6888-3.07790.2454530.18063920X-RAY DIFFRACTION100
3.0779-3.87770.20334580.16023945X-RAY DIFFRACTION100
3.8777-58.65490.21914330.1883974X-RAY DIFFRACTION100

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