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- PDB-8bgn: N,N-diacetylchitobiose deacetylase from Pyrococcus chitonophagus -

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Basic information

Entry
Database: PDB / ID: 8bgn
TitleN,N-diacetylchitobiose deacetylase from Pyrococcus chitonophagus
ComponentsDiacetylchitobiose deacetylase
KeywordsHYDROLASE / hyperthermophile
Function / homologyN-acetylglucosaminyl phosphatidylinositol deacetylase-related / Putative deacetylase LmbE-like domain superfamily / GlcNAc-PI de-N-acetylase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / metal ion binding / Diacetylchitobiose deacetylase
Function and homology information
Biological speciesThermococcus chitonophagus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsRypniewski, W. / Bejger, M. / Biniek-Antosiak, K.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreUMO-2017/27/B/NZ1/02201 Poland
CitationJournal: Int J Mol Sci / Year: 2022
Title: Structural, Thermodynamic and Enzymatic Characterization of N , N -Diacetylchitobiose Deacetylase from Pyrococcus chitonophagus.
Authors: Biniek-Antosiak, K. / Bejger, M. / Sliwiak, J. / Baranowski, D. / Mohammed, A.S.A. / Svergun, D.I. / Rypniewski, W.
History
DepositionOct 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diacetylchitobiose deacetylase
B: Diacetylchitobiose deacetylase
C: Diacetylchitobiose deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,43012
Polymers92,9153
Non-polymers5159
Water1,62190
1
A: Diacetylchitobiose deacetylase
B: Diacetylchitobiose deacetylase
C: Diacetylchitobiose deacetylase
hetero molecules

A: Diacetylchitobiose deacetylase
B: Diacetylchitobiose deacetylase
C: Diacetylchitobiose deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,86024
Polymers185,8306
Non-polymers1,03118
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area32660 Å2
ΔGint-409 kcal/mol
Surface area53140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.613, 150.613, 72.228
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

21A-432-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 2 - 267 / Label seq-ID: 2 - 267

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Diacetylchitobiose deacetylase


Mass: 30971.605 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus chitonophagus (archaea) / Gene: A3L04_02905, CHITON_0574 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A160VQZ8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.56 Å3/Da / Density % sol: 51.88 %
Crystal growTemperature: 308 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES, pH7.5, 2% v/v PEG 400, 2.0M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9797 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.76→49.3 Å / Num. obs: 24234 / % possible obs: 99.08 % / Redundancy: 19.4 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 18.4
Reflection shellResolution: 2.76→2.86 Å / Rmerge(I) obs: 0.966 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2190

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Processing

Software
NameVersionClassification
XDS5.8.0253data reduction
XSCALE3.27data scaling
Cootmodel building
PHASERphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XM0

4xm0


Resolution: 2.76→49.3 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 14.411 / SU ML: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2271 1001 4.1 %RANDOM
Rwork0.1763 ---
obs0.1784 23220 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 156.84 Å2 / Biso mean: 72.754 Å2 / Biso min: 38.83 Å2
Baniso -1Baniso -2Baniso -3
1--2.05 Å2-1.03 Å20 Å2
2---2.05 Å2-0 Å2
3---6.67 Å2
Refinement stepCycle: final / Resolution: 2.76→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6528 0 21 90 6639
Biso mean--88.29 62.25 -
Num. residues----798
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0136717
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176287
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.6539101
X-RAY DIFFRACTIONr_angle_other_deg1.2211.57914591
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0435795
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83522.149363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.553151164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0361542
X-RAY DIFFRACTIONr_chiral_restr0.0710.2855
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027413
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021449
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A87840.07
12B87840.07
21A86910.08
22C86910.08
31B87020.08
32C87020.08
LS refinement shellResolution: 2.763→2.835 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 65 -
Rwork0.36 1492 -
all-1557 -
obs--86.69 %

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