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- PDB-6h8n: Structure of peptidoglycan deacetylase PdaC from Bacillus subtili... -

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Basic information

Entry
Database: PDB / ID: 6h8n
TitleStructure of peptidoglycan deacetylase PdaC from Bacillus subtilis - mutant D285S
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 ...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
PHOSPHATE ION / Peptidoglycan-N-acetylmuramic acid deacetylase PdaC
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 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_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

Downloads & links

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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)49,5739
Polymers48,9732
Non-polymers6007
Water8,413467
1
A: Peptidoglycan-N-acetylmuramic acid deacetylase PdaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8345
Polymers24,4871
Non-polymers3474
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)24,7394
Polymers24,4871
Non-polymers2523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.420, 61.800, 130.990
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: 24486.746 Da / Num. of mol.: 2 / Mutation: D285S
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.4 M Ammonium phosphate monobasic

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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: 1.26→22.11 Å / Num. obs: 120462 / % possible obs: 99 % / Redundancy: 5.7 % / Biso Wilson estimate: 12.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06804 / Rrim(I) all: 0.07441 / Net I/σ(I): 11.01
Reflection shellResolution: 1.26→1.3 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.4831 / Mean I/σ(I) obs: 1.74 / Num. unique obs: 10846 / CC1/2: 0.707 / Rrim(I) all: 0.595 / % possible all: 89

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Processing

Software
NameVersionClassification
PHENIX(dev_2219: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H8L

6h8l


Resolution: 1.26→22.116 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 17.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1745 11264 4.92 %Random selection
Rwork0.16 ---
obs0.1607 114541 97.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.26→22.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3254 0 29 467 3750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073431
X-RAY DIFFRACTIONf_angle_d0.9774668
X-RAY DIFFRACTIONf_dihedral_angle_d22.6591329
X-RAY DIFFRACTIONf_chiral_restr0.074522
X-RAY DIFFRACTIONf_plane_restr0.006604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26-1.27430.31962950.32445574X-RAY DIFFRACTION76
1.2743-1.28930.31713430.31516230X-RAY DIFFRACTION83
1.2893-1.3050.29773350.30826589X-RAY DIFFRACTION89
1.305-1.32160.30113570.28936913X-RAY DIFFRACTION93
1.3216-1.33890.30193750.27527150X-RAY DIFFRACTION96
1.3389-1.35730.25653630.25747246X-RAY DIFFRACTION98
1.3573-1.37670.25273940.2477370X-RAY DIFFRACTION99
1.3767-1.39720.25074090.23087402X-RAY DIFFRACTION100
1.3972-1.4190.22773620.21947477X-RAY DIFFRACTION100
1.419-1.44230.23224000.2047408X-RAY DIFFRACTION100
1.4423-1.46720.21453960.1927408X-RAY DIFFRACTION100
1.4672-1.49380.20433680.1887480X-RAY DIFFRACTION100
1.4938-1.52260.19643890.18217392X-RAY DIFFRACTION100
1.5226-1.55360.19274460.17047332X-RAY DIFFRACTION100
1.5536-1.58740.18833980.16717464X-RAY DIFFRACTION100
1.5874-1.62430.16793950.15467403X-RAY DIFFRACTION100
1.6243-1.66490.16793440.15317478X-RAY DIFFRACTION100
1.6649-1.70990.14573540.14847423X-RAY DIFFRACTION100
1.7099-1.76020.15454020.14217468X-RAY DIFFRACTION100
1.7602-1.8170.1734150.14367349X-RAY DIFFRACTION100
1.817-1.88190.15173860.14347423X-RAY DIFFRACTION100
1.8819-1.95720.17193960.13867405X-RAY DIFFRACTION100
1.9572-2.04630.14363700.1377462X-RAY DIFFRACTION100
2.0463-2.15410.15713850.13317402X-RAY DIFFRACTION100
2.1541-2.28890.13053710.12897417X-RAY DIFFRACTION100
2.2889-2.46540.16553340.13577473X-RAY DIFFRACTION100
2.4654-2.71310.16183910.14367393X-RAY DIFFRACTION100
2.7131-3.10480.16383970.14897454X-RAY DIFFRACTION100
3.1048-3.90820.14973470.14977403X-RAY DIFFRACTION99
3.9082-22.11980.17063470.15357430X-RAY DIFFRACTION99

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