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- PDB-6hfz: Crystal structure of a two-domain esterase (CEX) active on acetyl... -

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Basic information

Entry
Database: PDB / ID: 6hfz
TitleCrystal structure of a two-domain esterase (CEX) active on acetylated mannans
ComponentsGDSL-like protein
KeywordsSUGAR BINDING PROTEIN / Esterase / carbohydrate / galactoglucomannan / deacetylation / biomass / gut flora
Function / homology
Function and homology information


acetylxylan esterase / hydrolase activity
Similarity search - Function
SGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Acetylxylan esterase
Similarity search - Component
Biological speciesRoseburia intestinalis L1-82 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsMichalak, L. / La Rosa, S.L. / Rohr, A.K. / Aachmann, F.L. / Westereng, B.
Funding support3items
OrganizationGrant numberCountry
Research Council of Norway244259
Research Council of Norway240967
Research Council of Norway226244/F50
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: A pair of esterases from a commensal gut bacterium remove acetylations from all positions on complex beta-mannans.
Authors: Michalak, L. / La Rosa, S.L. / Leivers, S. / Lindstad, L.J. / Rohr, A.K. / Lillelund Aachmann, F. / Westereng, B.
History
DepositionAug 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: GDSL-like protein
B: GDSL-like protein
C: GDSL-like protein
D: GDSL-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,43510
Polymers170,5434
Non-polymers8926
Water14,556808
1
A: GDSL-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9333
Polymers42,6361
Non-polymers2972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GDSL-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9333
Polymers42,6361
Non-polymers2972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GDSL-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6952
Polymers42,6361
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GDSL-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8742
Polymers42,6361
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.116, 136.516, 85.134
Angle α, β, γ (deg.)90.00, 115.09, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.938214, 0.177283, 0.297196), (0.212596, -0.382358, 0.899225), (0.273053, 0.906848, 0.321044)-180.19818, -66.76364, 84.10381

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Components

#1: Protein
GDSL-like protein


Mass: 42635.738 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Parts of this monomer is not well defined in the electron density map.
Source: (gene. exp.) Roseburia intestinalis L1-82 (bacteria)
Gene: ROSINTL182_05471 / Plasmid: pNIC-CH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C7G6F8
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 808 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.39 Å3/Da / Density % sol: 48.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M ammonium acetate, 0.1M HEPES pH 7.5 and 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97531 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97531 Å / Relative weight: 1
ReflectionResolution: 1.75→48.19 Å / Num. obs: 155949 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Net I/σ(I): 11.5
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.631 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7703 / CC1/2: 0.815 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
ARP/wARPmodel building
RESOLVEmodel building
AutoSolphasing
Aimless0.7.1data scaling
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.75→47.87 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.939 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.12 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23184 7628 4.9 %RANDOM
Rwork0.18976 ---
obs0.19178 148281 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.076 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å20.85 Å2
2---0.69 Å20 Å2
3----0.63 Å2
Refinement stepCycle: 1 / Resolution: 1.75→47.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11575 0 57 808 12440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01411922
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710519
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.66616180
X-RAY DIFFRACTIONr_angle_other_deg0.9361.66624652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1251469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36123.344631
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.415151915
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4261556
X-RAY DIFFRACTIONr_chiral_restr0.0780.21566
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213449
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022219
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_it3.0143.3825891
X-RAY DIFFRACTIONr_mcbond_other3.0133.3815890
X-RAY DIFFRACTIONr_mcangle_it4.1325.0637353
X-RAY DIFFRACTIONr_mcangle_other4.1325.0647354
X-RAY DIFFRACTIONr_scbond_it3.5583.7656031
X-RAY DIFFRACTIONr_scbond_other3.5563.7656031
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2165.4978828
X-RAY DIFFRACTIONr_long_range_B_refined6.92440.73513280
X-RAY DIFFRACTIONr_long_range_B_other6.91240.59313140
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 581 -
Rwork0.264 10942 -
obs--99.84 %

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