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- PDB-5emi: N-acetylmuramoyl-L-alanine amidase AmiC2 of Nostoc punctiforme -

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Basic information

Entry
Database: PDB / ID: 5emi
TitleN-acetylmuramoyl-L-alanine amidase AmiC2 of Nostoc punctiforme
ComponentsCell wall hydrolase/autolysin
KeywordsHYDROLASE / N-acetylmuramoyl-L-alanine amidase / multicellular cyanobacteria / peptidoglycan / nanopore formation
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / metal ion binding
Similarity search - Function
Zn-dependent exopeptidases / AMIN domain / AMIN domain / Ami_3 / N-acetylmuramoyl-L-alanine amidase, catalytic domain / N-acetylmuramoyl-L-alanine amidase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell wall hydrolase/autolysin
Similarity search - Component
Biological speciesNostoc punctiforme (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsBuettner, F.M. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation766 Germany
CitationJournal: Febs J. / Year: 2016
Title: Enabling cell-cell communication via nanopore formation: structure, function and localization of the unique cell wall amidase AmiC2 of Nostoc punctiforme.
Authors: Buttner, F.M. / Faulhaber, K. / Forchhammer, K. / Maldener, I. / Stehle, T.
History
DepositionNov 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Apr 20, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...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_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell wall hydrolase/autolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3095
Polymers19,8121
Non-polymers4974
Water3,207178
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-21 kcal/mol
Surface area8600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.030, 62.760, 65.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cell wall hydrolase/autolysin


Mass: 19811.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (strain ATCC 29133 / PCC 73102) (bacteria)
Gene: Npun_F1846 / Production host: Escherichia coli (E. coli)
References: UniProt: B2J2S4, 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-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.81 Å3/Da / Density % sol: 32.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 1 microL of protein (3.7 mg/ml) was mixed with 1 microL of well solution containing 120 mM alcohols (mixture of 1,6-hexanediol, 1-butanol, 1,2-propanediol, 2-propanol, 1,4-butanediol, and ...Details: 1 microL of protein (3.7 mg/ml) was mixed with 1 microL of well solution containing 120 mM alcohols (mixture of 1,6-hexanediol, 1-butanol, 1,2-propanediol, 2-propanol, 1,4-butanediol, and 1,3-propanediol), 100 mM MES/imidazole at pH 6.5, and 37.5 % PEG1000/PEG3350/MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.12→50 Å / Num. obs: 52924 / % possible obs: 94.3 % / Redundancy: 11.8 % / Biso Wilson estimate: 13.5 Å2 / CC1/2: 1 / Net I/σ(I): 31.54
Reflection shellResolution: 1.12→1.15 Å / Redundancy: 6.58 % / Mean I/σ(I) obs: 3.65 / CC1/2: 0.884 / % possible all: 69.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1jwq

1jwq


Resolution: 1.12→45.246 Å / SU ML: 0.05 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 11.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.146 2647 5 %
Rwork0.1342 --
obs0.1348 52922 94.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.12→45.246 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1387 0 29 178 1594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011465
X-RAY DIFFRACTIONf_angle_d1.4921987
X-RAY DIFFRACTIONf_dihedral_angle_d13.3569
X-RAY DIFFRACTIONf_chiral_restr0.079222
X-RAY DIFFRACTIONf_plane_restr0.006259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1202-1.14060.1722970.17421828X-RAY DIFFRACTION66
1.1406-1.16250.16971150.15382200X-RAY DIFFRACTION80
1.1625-1.18620.13691260.13922389X-RAY DIFFRACTION87
1.1862-1.2120.11391310.12962477X-RAY DIFFRACTION89
1.212-1.24020.11821330.12452545X-RAY DIFFRACTION92
1.2402-1.27120.10411360.1232576X-RAY DIFFRACTION93
1.2712-1.30560.13241380.12272615X-RAY DIFFRACTION94
1.3056-1.3440.12551400.12032662X-RAY DIFFRACTION96
1.344-1.38740.11231440.12052733X-RAY DIFFRACTION98
1.3874-1.4370.09921430.11272713X-RAY DIFFRACTION98
1.437-1.49460.1441440.10882752X-RAY DIFFRACTION99
1.4946-1.56260.12911470.10622792X-RAY DIFFRACTION100
1.5626-1.6450.12871480.10652804X-RAY DIFFRACTION100
1.645-1.7480.15351470.12242805X-RAY DIFFRACTION100
1.748-1.8830.1421480.13022803X-RAY DIFFRACTION100
1.883-2.07250.16591500.12342841X-RAY DIFFRACTION100
2.0725-2.37240.16291490.1362838X-RAY DIFFRACTION100
2.3724-2.98890.15471520.15792885X-RAY DIFFRACTION100
2.9889-45.28290.15471590.14883017X-RAY DIFFRACTION100

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