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- PDB-7y51: Acetylxylan esterase from Caldanaerobacter subterraneus subsp. te... -

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Basic information

Entry
Database: PDB / ID: 7y51
TitleAcetylxylan esterase from Caldanaerobacter subterraneus subsp. tengcongensis TTE0866 delta100 mutant
ComponentsPredicted xylanase/chitin deacetylase
KeywordsHYDROLASE / Acetylxylan esterase
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / hydrolase activity, acting on glycosyl bonds / xylan catabolic process
Similarity search - Function
Sporulation polysaccharide deacetylase PdaB-like / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel
Similarity search - Domain/homology
NICKEL (II) ION / Predicted xylanase/chitin deacetylase
Similarity search - Component
Biological speciesCaldanaerobacter subterraneus subsp. tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSasamoto, K. / Himiyama, T. / Moriyoshi, K. / Ohmoto, T. / Uegaki, K. / Nakamura, T. / Nishiya, Y.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K06616 Japan
Japan Society for the Promotion of Science (JSPS)20K15403 Japan
Japan Society for the Promotion of Science (JSPS)20K05740 Japan
CitationJournal: Febs Open Bio / Year: 2022
Title: Functional analysis of the N-terminal region of acetylxylan esterase from Caldanaerobacter subterraneus subsp. tengcongensis.
Authors: Sasamoto, K. / Himiyama, T. / Moriyoshi, K. / Ohmoto, T. / Uegaki, K. / Nakamura, T. / Nishiya, Y.
History
DepositionJun 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 19, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Predicted xylanase/chitin deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1253
Polymers22,9751
Non-polymers1512
Water61334
1
A: Predicted xylanase/chitin deacetylase
hetero molecules

A: Predicted xylanase/chitin deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2516
Polymers45,9492
Non-polymers3024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y+1/2,z1
Buried area3210 Å2
ΔGint-26 kcal/mol
Surface area15160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.090, 106.400, 117.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Predicted xylanase/chitin deacetylase / Acetylxylan esterase


Mass: 22974.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)
Strain: DSM 15242 / JCM 11007 / NBRC 100824 / MB4 / Gene: Cda1, TTE0866 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RBF4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.3 Å3/Da / Density % sol: 71.41 %
Crystal growTemperature: 293 K / Method: evaporation, recrystallization / pH: 8 / Details: 20 mM Tris-HCl (pH8.0) 100 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→39.91 Å / Num. obs: 14957 / % possible obs: 99.9 % / Redundancy: 11 % / CC1/2: 0.993 / Rmerge(I) obs: 0.17 / Net I/σ(I): 14.3
Reflection shellResolution: 2.45→2.55 Å / Rmerge(I) obs: 0.912 / Num. unique obs: 1651 / CC1/2: 0.84
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7FBW

7fbw


Resolution: 2.45→39.91 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.681 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.188
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2301 722 4.827 %
Rwork0.1907 14234 -
all0.193 --
obs-14956 99.906 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.227 Å2
Baniso -1Baniso -2Baniso -3
1-0.066 Å20 Å2-0 Å2
2---0.036 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.45→39.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1488 0 7 34 1529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131528
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171494
X-RAY DIFFRACTIONr_angle_refined_deg1.8681.6422067
X-RAY DIFFRACTIONr_angle_other_deg1.3441.5793468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5245185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.02124.17967
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.02715282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.244154
X-RAY DIFFRACTIONr_chiral_restr0.1050.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021660
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02308
X-RAY DIFFRACTIONr_nbd_refined0.2040.2295
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.21346
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2732
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2776
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.235
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0850.22
X-RAY DIFFRACTIONr_nbd_other0.1060.213
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0120.21
X-RAY DIFFRACTIONr_mcbond_it4.2843.66743
X-RAY DIFFRACTIONr_mcbond_other4.2123.654742
X-RAY DIFFRACTIONr_mcangle_it6.5075.478927
X-RAY DIFFRACTIONr_mcangle_other6.5215.481928
X-RAY DIFFRACTIONr_scbond_it4.994.328785
X-RAY DIFFRACTIONr_scbond_other4.9874.33786
X-RAY DIFFRACTIONr_scangle_it7.7276.231140
X-RAY DIFFRACTIONr_scangle_other7.7246.2321141
X-RAY DIFFRACTIONr_lrange_it9.8943.2611635
X-RAY DIFFRACTIONr_lrange_other9.8943.2871635
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.5140.296520.2651041X-RAY DIFFRACTION99.8174
2.514-2.5820.266470.2571029X-RAY DIFFRACTION99.9072
2.582-2.6570.29550.228961X-RAY DIFFRACTION100
2.657-2.7390.246540.225964X-RAY DIFFRACTION100
2.739-2.8290.29310.207928X-RAY DIFFRACTION100
2.829-2.9280.281480.199888X-RAY DIFFRACTION99.8933
2.928-3.0380.202540.205856X-RAY DIFFRACTION99.8902
3.038-3.1620.269410.216849X-RAY DIFFRACTION99.8878
3.162-3.3020.262470.204786X-RAY DIFFRACTION100
3.302-3.4630.262310.211771X-RAY DIFFRACTION100
3.463-3.650.251480.208719X-RAY DIFFRACTION99.8698
3.65-3.8710.285340.205704X-RAY DIFFRACTION100
3.871-4.1380.192340.166659X-RAY DIFFRACTION100
4.138-4.4680.187290.152608X-RAY DIFFRACTION99.8433
4.468-4.8930.142280.121571X-RAY DIFFRACTION100
4.893-5.4680.23210.163518X-RAY DIFFRACTION99.8148
5.468-6.3090.261190.185472X-RAY DIFFRACTION100
6.309-7.7140.195180.155408X-RAY DIFFRACTION100
7.714-10.8580.112210.12309X-RAY DIFFRACTION100
10.858-39.910.416100.266193X-RAY DIFFRACTION97.5962

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