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- PDB-2j13: Structure of a family 4 carbohydrate esterase from Bacillus anthracis -

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Basic information

Entry
Database: PDB / ID: 2j13
TitleStructure of a family 4 carbohydrate esterase from Bacillus anthracis
ComponentsPOLYSACCHARIDE DEACETYLASE
KeywordsHYDROLASE / FAMILY 4 / PEPTIDOGLYCAN / BACILLUS ANTHRACIS / BACTERIAL CELL WALL / CARBOHYDRATE ESTERASE
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / carbohydrate metabolic process / metal ion binding / membrane
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
ACETATE ION / CACODYLATE ION / Polysaccharide deacetylase / Polysaccharide deacetylase
Similarity search - Component
Biological speciesBACILLUS ANTHRACIS (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGloster, T.M. / Oberbarnscheidt, L. / Taylor, E.J. / Davies, G.J.
CitationJournal: Proteins: Struct., Funct., Bioinf. / Year: 2007
Title: Structure of a Carbohydrate Esterase from Bacillus Anthracis.
Authors: Oberbarnscheidt, L. / Taylor, E.J. / Davies, G.J. / Gloster, T.M.
History
DepositionAug 8, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_sheet
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _struct_sheet.number_strands
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
A: POLYSACCHARIDE DEACETYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0458
Polymers28,5281
Non-polymers5177
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)56.927, 56.927, 158.531
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein POLYSACCHARIDE DEACETYLASE / CARBOHYDRATE ESTERASE


Mass: 28528.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS ANTHRACIS (anthrax bacterium) / Strain: AMES / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q81Z49, UniProt: A0A6H3ACS3*PLUS, 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.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST 24 RESIDUES OF THE DEPOSITED SEQUENCE ARE PREDICTED TO CODE FOR A SIGNAL PEPTIDE WHICH ...THE FIRST 24 RESIDUES OF THE DEPOSITED SEQUENCE ARE PREDICTED TO CODE FOR A SIGNAL PEPTIDE WHICH WAS NOT INCLUDED IN THE CLONED SEQUENCE. THERE IS AN ADDITIONAL METHIONINE RESIDUE AT THE START OF THE CLONED SEQUENCE FROM THE EXPRESSION VECTOR.

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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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growpH: 6.5
Details: 0.1 M CACODYLATE, PH 6.5, 0.2 M ZINC ACETATE, 18% POLYETHYLENE GLYCOL 8K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 8, 2006 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 33502 / % possible obs: 99.2 % / Redundancy: 5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 25.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.2 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W1B

1w1b


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.804 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 13-22, 174-187 AND 236-237 CANNOT BE OBSERVED IN THE ELECTRON DENSITY AND HENCE ARE MISSING FROM THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1697 5.1 %RANDOM
Rwork0.186 ---
obs0.188 31740 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20.23 Å20 Å2
2--0.45 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1669 0 17 179 1865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221824
X-RAY DIFFRACTIONr_bond_other_d0.0070.021246
X-RAY DIFFRACTIONr_angle_refined_deg1.41.972485
X-RAY DIFFRACTIONr_angle_other_deg0.92233071
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.815236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27124.70685
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72115339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.094156
X-RAY DIFFRACTIONr_chiral_restr0.0840.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022015
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02367
X-RAY DIFFRACTIONr_nbd_refined0.2180.2352
X-RAY DIFFRACTIONr_nbd_other0.1920.21215
X-RAY DIFFRACTIONr_nbtor_refined0.1890.2842
X-RAY DIFFRACTIONr_nbtor_other0.0860.2923
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2119
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1170.27
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0860.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5731.51118
X-RAY DIFFRACTIONr_mcbond_other0.7191.5439
X-RAY DIFFRACTIONr_mcangle_it2.32321740
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9033831
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0914.5729
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 118 -
Rwork0.183 2194 -
obs--94.75 %

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