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- PDB-8c2o: Structure of E. coli AmiA -

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Basic information

Entry
Database: PDB / ID: 8c2o
TitleStructure of E. coli AmiA
ComponentsN-acetylmuramoyl-L-alanine amidase AmiA
KeywordsHYDROLASE / Monomer / Autoinhibited
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / cell wall organization / outer membrane-bounded periplasmic space / periplasmic space / zinc ion binding
Similarity search - Function
Ami_3 / N-acetylmuramoyl-L-alanine amidase, catalytic domain / N-acetylmuramoyl-L-alanine amidase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
N-acetylmuramoyl-L-alanine amidase AmiA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBaverstock, T.C. / Crow, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V017101/1 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Activator-induced conformational changes regulate division-associated peptidoglycan amidases.
Authors: Cook, J. / Baverstock, T.C. / McAndrew, M.B.L. / Roper, D.I. / Stansfeld, P.J. / Crow, A.
History
DepositionDec 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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 AmiA
B: N-acetylmuramoyl-L-alanine amidase AmiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3194
Polymers58,1892
Non-polymers1312
Water1,31573
1
A: N-acetylmuramoyl-L-alanine amidase AmiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1602
Polymers29,0941
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-acetylmuramoyl-L-alanine amidase AmiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1602
Polymers29,0941
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.515, 73.899, 115.563
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 56 - 280 / Label seq-ID: 23 - 247

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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


Mass: 29094.260 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: amiA, yfeE, b2435, JW2428 / Production host: Escherichia coli (E. coli) / Variant (production host): C43(DE3)
References: UniProt: P36548, N-acetylmuramoyl-L-alanine amidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: See paper for details.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→59.6 Å / Num. obs: 21955 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 51 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.05 / Net I/σ(I): 10.4
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 12.1 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2121 / CC1/2: 0.662 / Rpim(I) all: 0.506 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→59.586 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.16 / SU B: 7.389 / SU ML: 0.169 / Average fsc free: 0 / Average fsc work: 0 / Cross valid method: FREE R-VALUE / ESU R: 0.315 / ESU R Free: 0.234
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.236 1074 4.906 %
Rwork0.177 20819 -
all0.18 --
obs-21893 99.89 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 53.965 Å2
Baniso -1Baniso -2Baniso -3
1--1.445 Å20 Å2-0 Å2
2---0.646 Å2-0 Å2
3---2.09 Å2
Refinement stepCycle: LAST / Resolution: 2.35→59.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3498 0 2 73 3573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123578
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163477
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.6474836
X-RAY DIFFRACTIONr_angle_other_deg0.4741.5867992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4435456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.737526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.70110626
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.19610156
X-RAY DIFFRACTIONr_chiral_restr0.0690.2555
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024220
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02816
X-RAY DIFFRACTIONr_nbd_refined0.2130.2791
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.23134
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21786
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21979
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.297
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2380.212
X-RAY DIFFRACTIONr_nbd_other0.1950.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0740.25
X-RAY DIFFRACTIONr_mcbond_it5.0775.1411824
X-RAY DIFFRACTIONr_mcbond_other5.065.1421824
X-RAY DIFFRACTIONr_mcangle_it7.1519.2242280
X-RAY DIFFRACTIONr_mcangle_other7.159.2262281
X-RAY DIFFRACTIONr_scbond_it6.1645.8411754
X-RAY DIFFRACTIONr_scbond_other6.1625.8431755
X-RAY DIFFRACTIONr_scangle_it9.07110.3952556
X-RAY DIFFRACTIONr_scangle_other9.06910.3962557
X-RAY DIFFRACTIONr_lrange_it11.1552.0323965
X-RAY DIFFRACTIONr_lrange_other11.16352.0863954
X-RAY DIFFRACTIONr_ncsr_local_group_10.1050.057089
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.104650.05008
12AX-RAY DIFFRACTIONLocal ncs0.104650.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)WRfactor Rwork
2.35-2.4110.348940.27715230.281161999.87650.267
2.411-2.4770.306600.25314790.255154099.93510.238
2.477-2.5490.368640.23714460.242151199.93380.218
2.549-2.6270.3770.21113760.216145699.7940.193
2.627-2.7130.249800.20213480.205143299.72070.178
2.713-2.8080.276780.20512880.209136799.92680.178
2.808-2.9140.268660.18712480.191131999.62090.162
2.914-3.0320.263610.17112230.176128799.76690.147
3.032-3.1670.253570.17411890.177124799.91980.151
3.167-3.3210.212590.16111260.163118699.91570.139
3.321-3.50.268530.1610760.16411291000.142
3.5-3.7120.238620.16510110.16910731000.147
3.712-3.9670.257420.1579700.16110121000.143
3.967-4.2830.169550.1488880.1499431000.138
4.283-4.6890.167430.1348260.1368691000.129
4.689-5.2390.206350.1467640.1487991000.143
5.239-6.0420.223310.1966820.1977131000.187
6.042-7.380.225230.1785970.186201000.172
7.38-10.3580.232250.1614620.1654871000.165
10.358-59.5860.23390.2392970.23930799.67430.246

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