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- PDB-6agq: Acetyl xylan esterase from Paenibacillus sp. R4 -

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Basic information

Entry
Database: PDB / ID: 6agq
TitleAcetyl xylan esterase from Paenibacillus sp. R4
Componentsacetyl xylan esterase
KeywordsHYDROLASE / Paenibacillus sp. / Acetyl esterase / acetyl xylan esterases
Function / homology
Function and homology information


polysaccharide metabolic process / carboxylic ester hydrolase activity
Similarity search - Function
Acetyl xylan esterase / Carbohydrate esterase 7 family / Acetyl xylan esterase (AXE1) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Acetyl xylan esterase
Similarity search - Component
Biological speciesPaenibacillus sp. R4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsPark, S. / Lee, C.W. / Lee, J.H.
CitationJournal: PLoS ONE / Year: 2018
Title: Crystal structure and functional characterization of a cold-active acetyl xylan esterase (PbAcE) from psychrophilic soil microbe Paenibacillus sp.
Authors: Park, S.H. / Yoo, W. / Lee, C.W. / Jeong, C.S. / Shin, S.C. / Kim, H.W. / Park, H. / Kim, K.K. / Kim, T.D. / Lee, J.H.
History
DepositionAug 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _entity.formula_weight
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)217,46012
Polymers217,0686
Non-polymers3926
Water13,818767
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15920 Å2
ΔGint-278 kcal/mol
Surface area65310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.797, 141.659, 105.369
Angle α, β, γ (deg.)90.00, 104.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
acetyl xylan esterase


Mass: 36177.918 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus sp. R4 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A452CSP2*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 767 / 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: 2.6 Å3/Da / Density % sol: 52.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1.8 M sodium phosphate monobasic monohydrate, potassium phosphate dibasic pH 5.0

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 121844 / % possible obs: 96.8 % / Redundancy: 3.7 % / Net I/σ(I): 27.2
Reflection shellResolution: 2.1→2.14 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
MxDCdata collection
HKL-2000data scaling
Cootmodel building
RefinementResolution: 2.1→49.39 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.481 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.204 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25438 6247 5.1 %RANDOM
Rwork0.19824 ---
obs0.20116 115533 96.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.78 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.1→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15060 0 6 767 15833
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01915510
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213836
X-RAY DIFFRACTIONr_angle_refined_deg1.8061.95621096
X-RAY DIFFRACTIONr_angle_other_deg1.09332106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.05851890
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50523.36750
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.252152400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.96215102
X-RAY DIFFRACTIONr_chiral_restr0.1170.22172
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02117502
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023336
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8973.3657578
X-RAY DIFFRACTIONr_mcbond_other2.8963.3647577
X-RAY DIFFRACTIONr_mcangle_it3.9695.0369462
X-RAY DIFFRACTIONr_mcangle_other3.9695.0379463
X-RAY DIFFRACTIONr_scbond_it3.6733.8047932
X-RAY DIFFRACTIONr_scbond_other3.6733.8047933
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5875.54111635
X-RAY DIFFRACTIONr_long_range_B_refined7.12839.73717548
X-RAY DIFFRACTIONr_long_range_B_other7.09439.59217416
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.102→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 439 -
Rwork0.366 8000 -
obs--90.55 %

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