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- PDB-4nz4: Structure of Vibrio cholerae chitin de-N-acetylase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4nz4
TitleStructure of Vibrio cholerae chitin de-N-acetylase in complex with 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE (NDG) and zinc ion
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
ACETATE ION / 2-acetamido-2-deoxy-alpha-D-glucopyranose / :
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.944 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
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 2.2Oct 30, 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)94,98814
Polymers93,8482
Non-polymers1,14012
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-109 kcal/mol
Surface area29310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.478, 111.849, 69.043
Angle α, β, γ (deg.)90.00, 93.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Deacetylase DA1


Mass: 46923.922 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, UNP RESIDUES 23-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: M7M1G8, chitin deacetylase
#5: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 481 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 80mM MES pH 6.5, 0.16M Ca(OAc)2, 14.4% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.75 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: 1.75 Å / Relative weight: 1
ReflectionResolution: 1.94→47.35 Å / Num. obs: 64954 / % possible obs: 96.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.83 % / Biso Wilson estimate: 22.82 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 7.07
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 3.17 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.02 / % possible all: 94.9

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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: 1.944→47.348 Å / SU ML: 0.21 / σ(F): 1.36 / Phase error: 22.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2108 3239 4.99 %
Rwork0.1659 --
obs0.1681 64950 94.95 %
all-64950 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.944→47.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6282 0 66 471 6819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126559
X-RAY DIFFRACTIONf_angle_d1.3358958
X-RAY DIFFRACTIONf_dihedral_angle_d13.1332301
X-RAY DIFFRACTIONf_chiral_restr0.077971
X-RAY DIFFRACTIONf_plane_restr0.0071168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9442-1.97330.266720.23831418X-RAY DIFFRACTION50
1.9733-2.00410.30111240.2332688X-RAY DIFFRACTION96
2.0041-2.03690.26911400.2342703X-RAY DIFFRACTION95
2.0369-2.07210.27471470.24662645X-RAY DIFFRACTION94
2.0721-2.10970.29121430.24812601X-RAY DIFFRACTION92
2.1097-2.15030.27991460.2352600X-RAY DIFFRACTION93
2.1503-2.19420.28061260.22552723X-RAY DIFFRACTION96
2.1942-2.24190.28731510.21522687X-RAY DIFFRACTION96
2.2419-2.29410.29111390.20882718X-RAY DIFFRACTION96
2.2941-2.35140.26091270.1962705X-RAY DIFFRACTION96
2.3514-2.4150.24431480.1722681X-RAY DIFFRACTION96
2.415-2.48610.2131620.16992725X-RAY DIFFRACTION97
2.4861-2.56630.22651340.16542839X-RAY DIFFRACTION99
2.5663-2.6580.23221460.1622788X-RAY DIFFRACTION99
2.658-2.76450.20871400.15292796X-RAY DIFFRACTION99
2.7645-2.89030.19141390.1522806X-RAY DIFFRACTION99
2.8903-3.04260.20421330.1592765X-RAY DIFFRACTION97
3.0426-3.23320.19731360.15872819X-RAY DIFFRACTION100
3.2332-3.48280.20991620.15572786X-RAY DIFFRACTION99
3.4828-3.83310.17671570.14092803X-RAY DIFFRACTION99
3.8331-4.38740.17321520.12272800X-RAY DIFFRACTION99
4.3874-5.52630.14451490.12632804X-RAY DIFFRACTION99
5.5263-47.36160.18351660.16562811X-RAY DIFFRACTION98

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