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- PDB-4nz3: Structure of Vibrio cholerae chitin de-N-acetylase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4nz3
TitleStructure of Vibrio cholerae chitin de-N-acetylase in complex with DI(N-ACETYL-D-GLUCOSAMINE) (CBS) in P 21 21 21
ComponentsDeacetylase DA1
KeywordsHYDROLASE / (beta/alpha)7 / carbohydrate esterase
Function / homologySeminal 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 / :
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.114 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_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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / 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.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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 2.2Nov 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)95,19214
Polymers93,7922
Non-polymers1,40112
Water15,295849
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-65 kcal/mol
Surface area28800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.684, 98.142, 152.988
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) / 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


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 859 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.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 849 / 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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl pH 8.5, 0.1M MgCl2, 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: I04 / Wavelength: 0.9537 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 20, 2012
RadiationMonochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.11→29.711 Å / Num. obs: 54749 / % possible obs: 96.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 17.97 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 7.77
Reflection shellResolution: 2.11→2.19 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 2.82 / Num. unique all: 15366 / % possible all: 86.28

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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: 4NY2

4ny2


Resolution: 2.114→29.711 Å / SU ML: 0.23 / σ(F): 2.02 / Phase error: 18.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 2779 5.08 %RANDOM
Rwork0.1498 ---
all0.153 54749 --
obs0.153 54749 98.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.114→29.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6308 0 86 849 7243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146637
X-RAY DIFFRACTIONf_angle_d1.2539084
X-RAY DIFFRACTIONf_dihedral_angle_d14.042315
X-RAY DIFFRACTIONf_chiral_restr0.074982
X-RAY DIFFRACTIONf_plane_restr0.0061178
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1138-2.15020.27741020.2216186673
2.1502-2.18930.23961510.19282611100
2.1893-2.23140.2441400.17412582100
2.2314-2.27690.24741320.17342635100
2.2769-2.32640.27481350.16942578100
2.3264-2.38050.22131620.15572600100
2.3805-2.440.20911320.15652641100
2.44-2.5060.22971420.15952583100
2.506-2.57970.26611350.15832626100
2.5797-2.66290.22491580.15082603100
2.6629-2.7580.24241330.15612620100
2.758-2.86830.24321360.15672629100
2.8683-2.99880.23881270.15492657100
2.9988-3.15670.21411460.15462628100
3.1567-3.35420.20521370.14822639100
3.3542-3.61280.19781290.1401263199
3.6128-3.97560.1741520.1192263499
3.9756-4.54910.15511430.1134265499
4.5491-5.72470.16841290.12562729100
5.7247-29.7140.20961580.16882824100

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