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- PDB-7ddy: Crystal structure of an acetyl xylan esterase AlAXEase -

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Basic information

Entry
Database: PDB / ID: 7ddy
TitleCrystal structure of an acetyl xylan esterase AlAXEase
ComponentsG-D-S-L family lipolytic protein
KeywordsHYDROLASE / Acetyl xylan esterase / SGNH / carbohydrate esterase
Function / homologyLipase, GDSL, active site / Lipolytic enzymes "G-D-S-L" family, serine active site. / : / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / phosphatidylcholine lysophospholipase activity / lipid metabolic process / G-D-S-L family lipolytic protein
Function and homology information
Biological speciesArcticibacterium luteifluviistationis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.505 Å
AuthorsZhang, Y. / Li, P.Y. / Zhang, Y.Z.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Active site architecture of an acetyl xylan esterase indicates a novel cold adaptation strategy.
Authors: Zhang, Y. / Ding, H.T. / Jiang, W.X. / Zhang, X. / Cao, H.Y. / Wang, J.P. / Li, C.Y. / Huang, F. / Zhang, X.Y. / Chen, X.L. / Zhang, Y.Z. / Li, P.Y.
History
DepositionOct 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: G-D-S-L family lipolytic protein
A: G-D-S-L family lipolytic protein
B: G-D-S-L family lipolytic protein
C: G-D-S-L family lipolytic protein


Theoretical massNumber of molelcules
Total (without water)105,0844
Polymers105,0844
Non-polymers00
Water9,116506
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, tertramers in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.870, 80.610, 82.060
Angle α, β, γ (deg.)90.000, 103.130, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
G-D-S-L family lipolytic protein


Mass: 26271.020 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arcticibacterium luteifluviistationis (bacteria)
Gene: DJ013_06310 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2Z4G9P0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H2O

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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: 2.36 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 15% PEG 3350 0.1 M succinic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 33141 / % possible obs: 98.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.086 / Rrim(I) all: 0.162 / Net I/σ(I): 8.25
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 2.67 / Num. unique obs: 3086 / Rpim(I) all: 0.192 / Rrim(I) all: 0.362

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.505→49.327 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2344 1656 5 %
Rwork0.1752 31469 -
obs0.1781 33125 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.98 Å2 / Biso mean: 28.207 Å2 / Biso min: 11.29 Å2
Refinement stepCycle: final / Resolution: 2.505→49.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6326 0 0 506 6832
Biso mean---29.64 -
Num. residues----796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076429
X-RAY DIFFRACTIONf_angle_d0.9188669
X-RAY DIFFRACTIONf_chiral_restr0.053960
X-RAY DIFFRACTIONf_plane_restr0.0041133
X-RAY DIFFRACTIONf_dihedral_angle_d5.3423869
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5052-2.57890.26931350.1912240091
2.5789-2.66210.28811190.2041264699
2.6621-2.75730.26911490.2045260499
2.7573-2.86770.26421260.1952261898
2.8677-2.99820.22031210.1998262898
2.9982-3.15620.23941500.1937261799
3.1562-3.35390.27641450.1903261898
3.3539-3.61280.24111360.179263099
3.6128-3.97620.22541680.156262799
3.9762-4.55130.18841300.1464266499
4.5513-5.73270.21831320.14532693100
5.7327-49.3270.21091450.1787272499

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