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- PDB-6fkx: Crystal structure of an acetyl xylan esterase from a desert metagenome -

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Basic information

Entry
Database: PDB / ID: 6fkx
TitleCrystal structure of an acetyl xylan esterase from a desert metagenome
Components(Acetyl xylan ...) x 3
KeywordsHYDROLASE / Carbohydrate-active enzyme / acetyl xylan esterase / alpha-beta hydrolase / 7-ACA deacetylase
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / FORMIC ACID
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsAdesioye, F.A. / Makhalanyane, T.P. / Vikram, S. / Sewell, B.T. / Schubert, W. / Cowan, D.A.
Funding support South Africa, 1items
OrganizationGrant numberCountry
National Research Foundation (South Africa) South Africa
CitationJournal: Appl. Environ. Microbiol. / Year: 2018
Title: Structural Characterization and Directed Evolution of a Novel Acetyl Xylan Esterase Reveals Thermostability Determinants of the Carbohydrate Esterase 7 Family.
Authors: Adesioye, F.A. / Makhalanyane, T.P. / Vikram, S. / Sewell, B.T. / Schubert, W.D. / Cowan, D.A.
History
DepositionJan 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetyl xylan esterase
B: Acetyl xylan esterase
D: Acetyl xylan esterase
C: Acetyl xylan esterase
E: Acetyl xylan esterase
F: Acetyl xylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,32227
Polymers214,5046
Non-polymers2,81821
Water40,7862264
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20940 Å2
ΔGint-101 kcal/mol
Surface area64050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.680, 116.820, 159.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Acetyl xylan ... , 3 types, 6 molecules ABDEFC

#1: Protein Acetyl xylan esterase


Mass: 36036.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Namib Desert Soil Hypolith / Source: (gene. exp.) metagenome (others) / Plasmid: pET28a / Details (production host): Circular with 6X His-tags / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: acetylxylan esterase
#2: Protein
Acetyl xylan esterase


Mass: 35760.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Namib Desert Soil Hypolith / Source: (gene. exp.) metagenome (others) / Plasmid: pET28a / Details (production host): Circular 6X His-tag / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: acetylxylan esterase
#3: Protein Acetyl xylan esterase


Mass: 35426.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Namib Desert Soil Hypolith / Source: (gene. exp.) metagenome (others) / Plasmid: pET28a / Details (production host): Circular, 6X His-tag / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: acetylxylan esterase

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Non-polymers , 5 types, 2285 molecules

#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2264 / 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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M 2-(N-morpholino) ethanesulfonic acid (MES) buffers pH 8.5 and 25% PEG 8000 (w/v)
PH range: 6.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2016
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.026→89.23 Å / Num. obs: 130734 / % possible obs: 99.95 % / Redundancy: 2 % / Rmerge(I) obs: 0.06564 / Rpim(I) all: 0.06564 / Rrim(I) all: 0.09283 / Net I/σ(I): 10.02
Reflection shellResolution: 2.026→2.099 Å / Rmerge(I) obs: 0.3479 / Rpim(I) all: 0.3479 / Rrim(I) all: 0.4921

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FCY

3fcy


Resolution: 2.03→89.23 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2203 --
Rwork0.1692 --
obs-130719 99.95 %
Refinement stepCycle: LAST / Resolution: 2.03→89.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15134 0 112 2264 17510

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