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- PDB-1w1b: Structure of Bacillus subtilis PdaA with Cadmium, a family 4 Carb... -

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Basic information

Entry
Database: PDB / ID: 1w1b
TitleStructure of Bacillus subtilis PdaA with Cadmium, a family 4 Carbohydrate esterase.
ComponentsPROBABLE POLYSACCHARIDE DEACETYLASE PDAA
KeywordsHYDROLASE / FAMILY 4 CARBOHYDRATE ESTERASE / DEACETYLASE / PEPTIDOGLYCAN / NODB HOMOLOGY DOMAIN / SPORULATION
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 / MIRAS / Resolution: 2.1 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 18, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 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 1.4May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_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_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_conn.ptnr2_label_seq_id
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

Downloads & links

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Assembly

Deposited unit
1: PROBABLE POLYSACCHARIDE DEACETYLASE PDAA
2: PROBABLE POLYSACCHARIDE DEACETYLASE PDAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0386
Polymers58,5882
Non-polymers4504
Water6,215345
1
1: PROBABLE POLYSACCHARIDE DEACETYLASE PDAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5193
Polymers29,2941
Non-polymers2252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
2: PROBABLE POLYSACCHARIDE DEACETYLASE PDAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5193
Polymers29,2941
Non-polymers2252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)87.824, 87.824, 120.562
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: 29294.117 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
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O
Compound detailsREQUIRED FOR PRODUCTION OF MURAMIC DELTA-LACTAM RESIDUES IN THE SPORE CORTEX AND FOR GERMINATION.
Sequence detailsSIGNAL SEQUENCE REMOVED AND FIRST FIVE N-TERMINAL RESIDUES FROM MCS

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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: 46.31 %
Crystal growpH: 7.5 / Details: pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICRO / Wavelength: 1.5418
DetectorType: RIGAKU R-AXIS IV / Date: Nov 10, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 30220 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.6 / % possible all: 97.8

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.1→24.85 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.227 --RANDOM
Rwork0.179 ---
obs0.179 30220 98.5 %-
Solvent computationSolvent model: CNS BULK SOLVENT MODEL USED
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→24.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3846 0 4 345 4195
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_deg1.4
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: 2.1→25 Å / Total num. of bins used: 10

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