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- PDB-4hd5: Crystal Structure of BC0361, a polysaccharide deacetylase from Ba... -

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Basic information

Entry
Database: PDB / ID: 4hd5
TitleCrystal Structure of BC0361, a polysaccharide deacetylase from Bacillus cereus
ComponentsPolysaccharide deacetylase
KeywordsHYDROLASE / Tim Barrel / polysaccharide deacetylase
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Immunoglobulin-like - #3760 / Glycoside hydrolase/deacetylase / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich ...Immunoglobulin-like - #3760 / Glycoside hydrolase/deacetylase / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Polysaccharide deacetylase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFadouloglou, V.E. / Kokkinidis, M. / Glykos, N.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure determination through homology modelling and torsion-angle simulated annealing: application to a polysaccharide deacetylase from Bacillus cereus.
Authors: Fadouloglou, V.E. / Kapanidou, M. / Agiomirgianaki, A. / Arnaouteli, S. / Bouriotis, V. / Glykos, N.M. / Kokkinidis, M.
History
DepositionOct 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Mar 27, 2013Group: Database references
Revision 1.3Apr 3, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.pdbx_leaving_atom_flag / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)40,9963
Polymers40,8711
Non-polymers1242
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.455, 52.760, 93.638
Angle α, β, γ (deg.)90.00, 95.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Polysaccharide deacetylase


Mass: 40871.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / DSM 31 / Gene: BC0361, BC_0361 / Production host: Escherichia coli (E. coli) / References: UniProt: Q81IM3
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 25-30% (w/v) PEG3350, 100mM Tris/HCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K
PH range: 7.5-8.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU RUH3R11.5418
ROTATING ANODERIGAKU RUH3R21.5418
Detector
TypeIDDetectorDetails
MAR scanner 300 mm plate1IMAGE PLATEmirrors
MAR scanner 300 mm plate2IMAGE PLATEmirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1YALE MIRRORSSINGLE WAVELENGTHMx-ray1
2YALE MIRRORSSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→46.47 Å / Num. all: 21606 / Num. obs: 21606 / % possible obs: 81.34 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→1.95 Å / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 3.2 / % possible all: 59.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SAM-T08- PHASER - CNSmodel building
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
SAM-T08- PHASER - CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HOMOLOGY MODELING

Resolution: 1.9→46.47 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.527 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.149 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20252 1142 5 %RANDOM
Rwork0.17836 ---
obs0.17959 21606 81.34 %-
all-21606 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.301 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å2-0 Å2-0.38 Å2
2--0.25 Å20 Å2
3----0.43 Å2
Refine analyze
FreeObs
Luzzati sigma a0.149 Å0.186 Å
Refinement stepCycle: LAST / Resolution: 1.9→46.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2540 0 5 162 2707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192600
X-RAY DIFFRACTIONr_bond_other_d0.0010.022494
X-RAY DIFFRACTIONr_angle_refined_deg1.0971.9593505
X-RAY DIFFRACTIONr_angle_other_deg0.735790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8815317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.62425.424118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94315495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.698157
X-RAY DIFFRACTIONr_chiral_restr0.0640.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022883
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02560
LS refinement shellResolution: 1.9→1.952 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 69 -
Rwork0.211 1159 -
obs--59.79 %
Refinement TLS params.Method: refined / Origin x: 17.197 Å / Origin y: -10.567 Å / Origin z: 212.429 Å
111213212223313233
T0.0426 Å20.0083 Å20.005 Å2-0.0075 Å20.0084 Å2--0.0112 Å2
L0.1424 °2-0.0146 °2-0.0541 °2-1.0222 °20.2813 °2--0.6415 °2
S-0.0069 Å °0.018 Å °0.0232 Å °-0.1204 Å °0.0081 Å °0.0091 Å °0.0797 Å °0.0247 Å °-0.0012 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A45 - 87
2X-RAY DIFFRACTION1A88 - 140
3X-RAY DIFFRACTION1A141 - 227
4X-RAY DIFFRACTION1A228 - 360
5X-RAY DIFFRACTION1A401
6X-RAY DIFFRACTION1A402

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