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- PDB-4knk: Crystal structure of Staphylococcus aureus hydrolase AmiA -

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Basic information

Entry
Database: PDB / ID: 4knk
TitleCrystal structure of Staphylococcus aureus hydrolase AmiA
ComponentsBifunctional autolysin
KeywordsHYDROLASE / peptidoglycan / autolysin / amidase / N-acetylmuramoyl-L-alanine amidase
Function / homology
Function and homology information


mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity / N-acetylmuramoyl-L-alanine amidase / amidase activity / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / cell wall organization / extracellular region
Similarity search - Function
: / Lysozyme subfamily 2 / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile. / Lysozyme-like / Peptidoglycan recognition protein-like ...: / Lysozyme subfamily 2 / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile. / 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
FORMIC ACID / IMIDAZOLE / DI(HYDROXYETHYL)ETHER / Bifunctional autolysin
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.124 Å
AuthorsBuettner, F.M. / Zoll, S. / Stehle, T.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structure-function analysis of Staphylococcus aureus amidase reveals the determinants of peptidoglycan recognition and cleavage.
Authors: Buttner, F.M. / Zoll, S. / Nega, M. / Gotz, F. / Stehle, T.
History
DepositionMay 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / struct_ref_seq_dif / struct_site
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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_ref_seq_dif.details / _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: Bifunctional autolysin
B: Bifunctional autolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,25914
Polymers50,5322
Non-polymers72712
Water9,638535
1
A: Bifunctional autolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6387
Polymers25,2661
Non-polymers3726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional autolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6227
Polymers25,2661
Non-polymers3566
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.800, 81.680, 68.690
Angle α, β, γ (deg.)90.00, 128.84, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-858-

HOH

21B-861-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bifunctional autolysin / N-acetylmuramoyl-L-alanine amidase / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / AmiA


Mass: 25265.828 Da / Num. of mol.: 2 / Fragment: UNP residues 198-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: NCTC 8325 / Gene: atl, nag, SAOUHSC_00994 / Plasmid: pGEX-4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2FZK7, N-acetylmuramoyl-L-alanine amidase, mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase

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Non-polymers , 7 types, 547 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 535 / 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: 2.09 Å3/Da / Density % sol: 41.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES/imidazole, pH 6.5, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M sodium citrate, 0.02 M racemic sodium/potassium tartrate, 0.02 M sodium oxamate, 12.5% w/v PEG1000, 12.5% ...Details: 0.1 M MES/imidazole, pH 6.5, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M sodium citrate, 0.02 M racemic sodium/potassium tartrate, 0.02 M sodium oxamate, 12.5% w/v PEG1000, 12.5% w/v PEG3350, 12.5% w/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 9, 2011
RadiationMonochromator: Bartels Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.12→48.164 Å / Num. all: 158107 / Num. obs: 146370 / % possible obs: 92.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 13.7 Å2 / Net I/σ(I): 21.1
Reflection shellResolution: 1.12→1.15 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 6937 / % possible all: 59.7

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LAT

3lat


Resolution: 1.124→40.84 Å / SU ML: 0.07 / σ(F): 1.99 / Phase error: 12.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1389 7319 5 %RANDOM
Rwork0.1209 ---
obs0.1218 146365 92.9 %-
all-158366 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.124→40.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3285 0 41 535 3861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093457
X-RAY DIFFRACTIONf_angle_d1.3284718
X-RAY DIFFRACTIONf_dihedral_angle_d12.2071213
X-RAY DIFFRACTIONf_chiral_restr0.084481
X-RAY DIFFRACTIONf_plane_restr0.008623
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.124-1.13680.25111140.25192167X-RAY DIFFRACTION44
1.1368-1.15020.2461910.21093632X-RAY DIFFRACTION72
1.1502-1.16420.21732020.17473836X-RAY DIFFRACTION78
1.1642-1.17890.18882160.15214108X-RAY DIFFRACTION83
1.1789-1.19440.17052280.15014333X-RAY DIFFRACTION87
1.1944-1.21080.16652300.14654358X-RAY DIFFRACTION88
1.2108-1.22810.16062330.13354435X-RAY DIFFRACTION89
1.2281-1.24640.16862340.1264451X-RAY DIFFRACTION90
1.2464-1.26590.15072450.12694649X-RAY DIFFRACTION93
1.2659-1.28670.14172440.12224636X-RAY DIFFRACTION94
1.2867-1.30880.15992470.11784690X-RAY DIFFRACTION95
1.3088-1.33270.1372510.11254769X-RAY DIFFRACTION96
1.3327-1.35830.14262510.11064765X-RAY DIFFRACTION96
1.3583-1.3860.14842530.10724816X-RAY DIFFRACTION96
1.386-1.41610.14442510.10574770X-RAY DIFFRACTION97
1.4161-1.44910.15962570.09874878X-RAY DIFFRACTION98
1.4491-1.48530.13252570.09444877X-RAY DIFFRACTION98
1.4853-1.52550.1222600.09544942X-RAY DIFFRACTION99
1.5255-1.57040.11742610.08854955X-RAY DIFFRACTION99
1.5704-1.62110.11462600.08834946X-RAY DIFFRACTION99
1.6211-1.6790.10922610.09254968X-RAY DIFFRACTION100
1.679-1.74620.12232620.10324966X-RAY DIFFRACTION100
1.7462-1.82570.13732630.10634998X-RAY DIFFRACTION100
1.8257-1.9220.13392620.10814986X-RAY DIFFRACTION100
1.922-2.04240.12142640.10945005X-RAY DIFFRACTION100
2.0424-2.20010.12632610.10944963X-RAY DIFFRACTION100
2.2001-2.42140.12822650.12285025X-RAY DIFFRACTION100
2.4214-2.77180.14312630.13535002X-RAY DIFFRACTION100
2.7718-3.49180.13862640.13525022X-RAY DIFFRACTION100
3.4918-40.8670.13982690.13335098X-RAY DIFFRACTION100

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