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- PDB-8bgp: N,N-diacetylchitobiose deacetylase from Pyrococcus chitonophagus ... -

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Basic information

Entry
Database: PDB / ID: 8bgp
TitleN,N-diacetylchitobiose deacetylase from Pyrococcus chitonophagus anomalous data
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: 2.51 Å
AuthorsRypniewski, W. / Biniek-Antosiak, K. / Bejger, M.
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
D: Diacetylchitobiose deacetylase
E: Diacetylchitobiose deacetylase
F: Diacetylchitobiose deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,61518
Polymers185,8306
Non-polymers78512
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30660 Å2
ΔGint-543 kcal/mol
Surface area54970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.642, 158.654, 158.517
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHELEULEUAA2 - 2662 - 266
21PHEPHELEULEUBB2 - 2662 - 266
12METMETILEILEAA1 - 2671 - 267
22METMETILEILECC1 - 2671 - 267
13METMETILEILEAA1 - 2671 - 267
23METMETILEILEDD1 - 2671 - 267
14METMETILEILEAA1 - 2671 - 267
24METMETILEILEEE1 - 2671 - 267
15PHEPHELEULEUAA2 - 2662 - 266
25PHEPHELEULEUFF2 - 2662 - 266
16PHEPHELEULEUBB2 - 2662 - 266
26PHEPHELEULEUCC2 - 2662 - 266
17PHEPHELEULEUBB2 - 2662 - 266
27PHEPHELEULEUDD2 - 2662 - 266
18PHEPHELEULEUBB2 - 2662 - 266
28PHEPHELEULEUEE2 - 2662 - 266
19PHEPHEILEILEBB2 - 2672 - 267
29PHEPHEILEILEFF2 - 2672 - 267
110METMETILEILECC1 - 2671 - 267
210METMETILEILEDD1 - 2671 - 267
111METMETILEILECC1 - 2671 - 267
211METMETILEILEEE1 - 2671 - 267
112PHEPHELEULEUCC2 - 2662 - 266
212PHEPHELEULEUFF2 - 2662 - 266
113METMETILEILEDD1 - 2671 - 267
213METMETILEILEEE1 - 2671 - 267
114PHEPHELEULEUDD2 - 2662 - 266
214PHEPHELEULEUFF2 - 2662 - 266
115PHEPHELEULEUEE2 - 2662 - 266
215PHEPHELEULEUFF2 - 2662 - 266

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Diacetylchitobiose deacetylase


Mass: 30971.605 Da / Num. of mol.: 6
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.: 12 / Source method: isolated from a natural source / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.66 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 308 K / Method: vapor diffusion, sitting drop
Details: 2.0M ammonium sulfate, 0.1M HEPES pH 7.5, 2% v/v PEG 400

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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: 1.2815 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2815 Å / Relative weight: 1
ReflectionResolution: 2.506→45.7 Å / Num. obs: 129806 / % possible obs: 97.3 % / Redundancy: 12.98 % / Rmerge(I) obs: 0.199 / Net I/σ(I): 11.052
Reflection shellResolution: 2.506→2.619 Å / Num. unique obs: 2179 / CC1/2: 0.4318

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Processing

Software
NameVersionClassification
XSCALEdata scaling
XDSdata reduction
Cootmodel building
PHASERphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8BGN

8bgn


Resolution: 2.51→45.7 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.868 / SU B: 11.696 / SU ML: 0.253 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.428 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2614 1145 2.6 %RANDOM
Rwork0.2183 ---
obs0.2194 42432 63.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.15 Å2 / Biso mean: 40.197 Å2 / Biso min: 12.71 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å20 Å2
2--2.42 Å2-0 Å2
3----1.32 Å2
Refinement stepCycle: final / Resolution: 2.51→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13088 0 12 17 13117
Biso mean--43.35 23.59 -
Num. residues----1600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01313442
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712570
X-RAY DIFFRACTIONr_angle_refined_deg1.4491.65118226
X-RAY DIFFRACTIONr_angle_other_deg1.1911.57829178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7251594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.58822.149726
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.835152340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5661584
X-RAY DIFFRACTIONr_chiral_restr0.0640.21714
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214854
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022902
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A86190.07
12B86190.07
21A87670.07
22C87670.07
31A87830.05
32D87830.05
41A87720.06
42E87720.06
51A87050.06
52F87050.06
61B85820.07
62C85820.07
71B86370.06
72D86370.06
81B86510.06
82E86510.06
91B87140.06
92F87140.06
101C87820.06
102D87820.06
111C87400.07
112E87400.07
121C86720.06
122F86720.06
131D87650.06
132E87650.06
141D87090.05
142F87090.05
151E87100.06
152F87100.06
LS refinement shellResolution: 2.51→2.571 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.277 43 -
Rwork0.2194 1103 -
obs--22.75 %

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