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- PDB-1w17: Structure of Bacillus subtilis PdaA, a family 4 Carbohydrate esterase. -

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Basic information

Entry
Database: PDB / ID: 1w17
TitleStructure of Bacillus subtilis PdaA, a family 4 Carbohydrate esterase.
ComponentsPROBABLE POLYSACCHARIDE DEACETYLASE PDAA
KeywordsHYDROLASE / FAMILY 4 CARBOHYDRATE ESTERASE / DEACETYLASE / PEPTIDOGLYCAN / NODB HOMOLOGY DOMAIN
Function / homology
Function and homology information


deacetylase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / sporulation resulting in formation of a cellular spore / cell wall organization / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Peptidoglycan-N-acetylmuramic acid deacetylase PdaA / : / 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
Peptidoglycan-N-acetylmuramic acid deacetylase PdaA
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.9 Å
AuthorsBlair, D.E. / van Aalten, D.M.F.
CitationJournal: FEBS Lett. / Year: 2004
Title: Structures of Bacillus subtilis PdaA, a family 4 carbohydrate esterase, and a complex with N-acetyl-glucosamine.
Authors: Blair, D.E. / van Aalten, D.M.
History
DepositionJun 17, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Advisory / Database references ...Advisory / Database references / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Item: _audit_author.name / _citation.page_last ..._audit_author.name / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5May 8, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROBABLE POLYSACCHARIDE DEACETYLASE PDAA
B: PROBABLE POLYSACCHARIDE DEACETYLASE PDAA


Theoretical massNumber of molelcules
Total (without water)60,2252
Polymers60,2252
Non-polymers00
Water6,593366
1
A: PROBABLE POLYSACCHARIDE DEACETYLASE PDAA


Theoretical massNumber of molelcules
Total (without water)30,1121
Polymers30,1121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PROBABLE POLYSACCHARIDE DEACETYLASE PDAA


Theoretical massNumber of molelcules
Total (without water)30,1121
Polymers30,1121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)88.115, 88.115, 120.957
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein PROBABLE POLYSACCHARIDE DEACETYLASE PDAA / PDAA


Mass: 30112.256 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: O34928, Hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.3 Å3/Da / Density % sol: 44.78 %
Crystal growpH: 7.5 / Details: 20%(W/V) PEG 12000, 0.1M HEPES PH7.5, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8123
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 24, 2003 / Details: MIRRORS
RadiationMonochromator: GERMANIUM TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. obs: 41729 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.9→14.98 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2285199.66 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.262 646 1.5 %RANDOM
Rwork0.201 ---
obs0.201 41703 99.9 %-
Solvent computationSolvent model: CNS BULK SOLVENT MODEL USED / Bsol: 47.5037 Å2 / ksol: 0.362716 e/Å3
Displacement parametersBiso mean: 26.35 Å2
Baniso -1Baniso -2Baniso -3
1-3.85 Å23.34 Å20 Å2
2--3.85 Å20 Å2
3----7.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.9→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3846 0 0 366 4212
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree: 0.261 / Rfactor Rwork: 0.201 / Total num. of bins used: 10
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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