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- PDB-4oui: Structure of Vibrio cholerae chitin de-N-acetylase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4oui
TitleStructure of Vibrio cholerae chitin de-N-acetylase in complex with TRIACETYLCHITOTRIOSE (CTO)
ComponentsDeacetylase DA1
KeywordsHYDROLASE / (BETA/ALPHA)7 / CARBOHYDRATE ESTERASE
Function / homology
Function and homology information


Seminal Fluid Protein PDC-109 (Domain B) - #90 / Glycoside hydrolase/deacetylase / Seminal Fluid Protein PDC-109 (Domain B) / Ribbon / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
triacetyl-beta-chitotriose / :
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsAlbesa-Jove, D. / Andres, E. / Biarnes, X. / Planas, A. / Guerin, M.E.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Structural basis of chitin oligosaccharide deacetylation.
Authors: Andres, E. / Albesa-Jove, D. / Biarnes, X. / Moerschbacher, B.M. / Guerin, M.E. / Planas, A.
History
DepositionFeb 17, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Structure summary
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_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.value / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deacetylase DA1
B: Deacetylase DA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,53713
Polymers93,7922
Non-polymers1,74511
Water12,917717
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-132 kcal/mol
Surface area29470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.100, 98.940, 154.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Deacetylase DA1


Mass: 46895.910 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, UNP RESIDUES 23-427 / Mutation: D39S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: VCNHCC010F_001593 / Production host: Escherichia coli (E. coli) / References: UniProt: M7M1G8, chitin deacetylase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 726 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 717 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M MgCl2, 0.1M TRIS pH 8.5, 17% (w/v) PEG 20000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2013
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.17→83.32 Å / Num. all: 52387 / Num. obs: 52387 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 11.925 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 12.7
Reflection shellResolution: 2.17→2.23 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3589 / % possible all: 92.8

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NZ4

4nz4


Resolution: 2.17→83.32 Å / SU ML: 0.24 / σ(F): 0.14 / Phase error: 21.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2136 5097 5.12 %RANDOM
Rwork0.1609 ---
all0.1636 52387 --
obs0.1636 52387 99.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.17→83.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6315 0 110 717 7142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0226671
X-RAY DIFFRACTIONf_angle_d1.3789146
X-RAY DIFFRACTIONf_dihedral_angle_d12.772310
X-RAY DIFFRACTIONf_chiral_restr0.075994
X-RAY DIFFRACTIONf_plane_restr0.0061180
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1701-2.19470.2991570.2786297292
2.1947-2.22050.35661780.2698295193
2.2205-2.24760.35161280.2606303895
2.2476-2.27610.32581640.2503306896
2.2761-2.3060.28231800.2403310097
2.306-2.33760.27341340.2209315499
2.3376-2.3710.27011880.21133207100
2.371-2.40640.25981870.19713144100
2.4064-2.4440.2271810.19253128100
2.444-2.48410.24481700.18373191100
2.4841-2.52690.26441440.17783202100
2.5269-2.57290.2461830.17433191100
2.5729-2.62240.23451980.1743138100
2.6224-2.67590.21791800.16993190100
2.6759-2.73410.23311680.16543164100
2.7341-2.79770.22351720.1553180100
2.7977-2.86770.24451670.15793170100
2.8677-2.94520.23281890.1593165100
2.9452-3.03190.23521500.15753189100
3.0319-3.12970.21651790.15453150100
3.1297-3.24160.26071490.16433212100
3.2416-3.37140.19741610.14923196100
3.3714-3.52480.20741900.15113151100
3.5248-3.71070.19821470.13593178100
3.7107-3.94320.17491860.12063165100
3.9432-4.24760.12351420.11813214100
4.2476-4.6750.14071710.10883158100
4.675-5.35140.16591940.11943171100
5.3514-6.74170.19461840.15293153100
6.7417-83.38110.18291760.1662315399

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