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- PDB-6h8l: Structure of peptidoglycan deacetylase PdaC from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 6h8l
TitleStructure of peptidoglycan deacetylase PdaC from Bacillus subtilis
ComponentsPeptidoglycan-N-acetylmuramic acid deacetylase PdaC
KeywordsHYDROLASE / Deacetylase
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / carbohydrate metabolic process / metal ion binding / plasma membrane
Similarity search - Function
Peptidoglycan GlcNAc deacetylase / Deacetylase PdaC / Deacetylase PdaC / Domain of unknown function DUF3298 / PdaC/RsiV-like superfamily / Protein of unknown function (DUF3298) / Glycoside hydrolase/deacetylase / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase ...Peptidoglycan GlcNAc deacetylase / Deacetylase PdaC / Deacetylase PdaC / Domain of unknown function DUF3298 / PdaC/RsiV-like superfamily / Protein of unknown function (DUF3298) / Glycoside hydrolase/deacetylase / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Peptidoglycan-N-acetylmuramic acid deacetylase PdaC
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsSainz-Polo, M.A. / Grifoll-Romero, L. / Albesa-Jove, D. / Planas, A. / Guerin, M.E.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structure-function relationships underlying the dualN-acetylmuramic andN-acetylglucosamine specificities of the bacterial peptidoglycan deacetylase PdaC.
Authors: Grifoll-Romero, L. / Sainz-Polo, M.A. / Albesa-Jove, D. / Guerin, M.E. / Biarnes, X. / Planas, A.
History
DepositionAug 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 17, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidoglycan-N-acetylmuramic acid deacetylase PdaC
B: Peptidoglycan-N-acetylmuramic acid deacetylase PdaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4616
Polymers49,0302
Non-polymers4314
Water7,170398
1
A: Peptidoglycan-N-acetylmuramic acid deacetylase PdaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7303
Polymers24,5151
Non-polymers2152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidoglycan-N-acetylmuramic acid deacetylase PdaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7303
Polymers24,5151
Non-polymers2152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.346, 61.916, 132.226
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 Peptidoglycan-N-acetylmuramic acid deacetylase PdaC / Peptidoglycan MurNAc deacetylase / Polysaccharide deacetylase PdaC


Mass: 24514.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: pdaC, yjeA, BSU12100 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O34798, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#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: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.2 M ammonium tartrate dibasic pH 6.6, 20% (w/v) polyethylene glycol 3.350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.54→56.07 Å / Num. obs: 67783 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 17.77 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0877 / Rrim(I) all: 0.0957 / Net I/σ(I): 11.39
Reflection shellResolution: 1.54→1.59 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.8135 / Mean I/σ(I) obs: 2.04 / Num. unique obs: 6689 / CC1/2: 0.713 / Rrim(I) all: 0.8819 / % possible all: 100

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Processing

Software
NameClassification
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C1G

2c1g


Resolution: 1.54→56.07 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.9
RfactorNum. reflection% reflectionSelection details
Rfree0.1944 3327 4.91 %Random selection
Rwork0.1749 ---
obs0.1759 67779 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.24 Å2
Refinement stepCycle: LAST / Resolution: 1.54→56.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3242 0 22 398 3662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053364
X-RAY DIFFRACTIONf_angle_d0.7894575
X-RAY DIFFRACTIONf_dihedral_angle_d14.4392062
X-RAY DIFFRACTIONf_chiral_restr0.047519
X-RAY DIFFRACTIONf_plane_restr0.005595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5414-1.56340.27841310.24822637X-RAY DIFFRACTION100
1.5634-1.58680.23891360.23892659X-RAY DIFFRACTION100
1.5868-1.61160.25991330.22672634X-RAY DIFFRACTION100
1.6116-1.6380.25581280.22162682X-RAY DIFFRACTION100
1.638-1.66620.20351240.20652662X-RAY DIFFRACTION100
1.6662-1.69650.23661570.20312641X-RAY DIFFRACTION100
1.6965-1.72920.21621410.19572661X-RAY DIFFRACTION100
1.7292-1.76450.23661470.18732641X-RAY DIFFRACTION100
1.7645-1.80280.24051460.18352635X-RAY DIFFRACTION100
1.8028-1.84480.24491460.18322668X-RAY DIFFRACTION100
1.8448-1.89090.21741370.182673X-RAY DIFFRACTION100
1.8909-1.9420.19031430.17852649X-RAY DIFFRACTION100
1.942-1.99920.21861130.17472710X-RAY DIFFRACTION100
1.9992-2.06370.16151290.16532685X-RAY DIFFRACTION100
2.0637-2.13750.1881290.16282687X-RAY DIFFRACTION100
2.1375-2.22310.16531400.15852663X-RAY DIFFRACTION100
2.2231-2.32420.16671300.1582694X-RAY DIFFRACTION100
2.3242-2.44680.18371410.16532686X-RAY DIFFRACTION100
2.4468-2.60010.21071500.16442696X-RAY DIFFRACTION100
2.6001-2.80080.17821560.17152689X-RAY DIFFRACTION100
2.8008-3.08270.21440.182726X-RAY DIFFRACTION100
3.0827-3.52870.21681360.17532710X-RAY DIFFRACTION100
3.5287-4.44550.16751360.15542769X-RAY DIFFRACTION99
4.4455-56.11010.17591540.18072895X-RAY DIFFRACTION100

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