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

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Basic information

Entry
Database: PDB / ID: 4nyu
TitleStructure of Vibrio cholerae chitin de-N-acetylase in complex with acetate ion (ACT) in C 2 2 21
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
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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
DepositionDec 11, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Structure summary
Revision 1.2Nov 8, 2023Group: 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 / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deacetylase DA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,91713
Polymers46,9241
Non-polymers99312
Water7,656425
1
A: Deacetylase DA1
hetero molecules

A: Deacetylase DA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,83526
Polymers93,8482
Non-polymers1,98724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area6230 Å2
ΔGint-126 kcal/mol
Surface area31960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.528, 108.191, 93.858
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-508-

GOL

21A-883-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Deacetylase DA1


Mass: 46923.922 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, UNP RESIDUES 23-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: deaA, VCNHCC010F_001593 / Production host: Escherichia coli (E. coli) / References: UniProt: M7M1G8, chitin deacetylase

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Non-polymers , 5 types, 437 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M sodium cacodylate, 0.2M Ca(OAc)2 and 18% (w/v) PEG 8000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 4, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.03→100 Å / Num. all: 27231 / Num. obs: 27231 / % possible obs: 95.58 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 20.87 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 10.11
Reflection shellResolution: 2.03→2.1 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 2.35 / Num. unique all: 2169 / % possible all: 80.33

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NY2

4ny2


Resolution: 2.03→46.868 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 22.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2281 1382 5.08 %RANDOM
Rwork0.1795 ---
all0.182 27224 --
obs0.182 27224 95.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.03→46.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3144 0 60 425 3629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063327
X-RAY DIFFRACTIONf_angle_d0.6714536
X-RAY DIFFRACTIONf_dihedral_angle_d12.1881162
X-RAY DIFFRACTIONf_chiral_restr0.042488
X-RAY DIFFRACTIONf_plane_restr0.003591
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.03-2.10260.3171230.2349213280
2.1026-2.18680.2561340.2083249694
2.1868-2.28630.23371470.192265399
2.2863-2.40680.27371320.1885266399
2.4068-2.55760.26631350.183263398
2.5576-2.75510.2541380.197267699
2.7551-3.03230.23061540.1871259897
3.0323-3.47090.21831480.1763262797
3.4709-4.37250.19841380.1482264296
4.3725-46.88070.18631330.1727272295

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