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- PDB-6hh9: Crystal structure of a two-domain esterase (CEX) active on acetyl... -

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Basic information

Entry
Database: PDB / ID: 6hh9
TitleCrystal structure of a two-domain esterase (CEX) active on acetylated mannans co-crystallized with mannopentaose
ComponentsGDSL-like protein
KeywordsSUGAR BINDING PROTEIN / Esterase / carbohydrate / galactoglucomannan / deacetylation / biomass / gut flora
Function / homologySGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / GDSL-like protein
Function and homology information
Biological speciesRoseburia intestinalis L1-82 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMichalak, L. / La Rosa, S.L. / Rohr, A.K. / Aachmann, F.L. / Westereng, B.
Funding support Norway, 3items
OrganizationGrant numberCountry
Research Council of Norway244259 Norway
Research Council of Norway240967 Norway
Research Council of Norway226244/F50 Norway
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 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)171,7858
Polymers169,6054
Non-polymers2,1804
Water8,773487
1
A: GDSL-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0682
Polymers42,4011
Non-polymers6671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GDSL-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9062
Polymers42,4011
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GDSL-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9062
Polymers42,4011
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GDSL-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9062
Polymers42,4011
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.482, 136.690, 85.411
Angle α, β, γ (deg.)90.00, 113.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
GDSL-like protein


Mass: 42401.270 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseburia intestinalis L1-82 (bacteria)
Gene: ROSINTL182_05471 / Plasmid: pNIC-CH / Production host: Escherichia coli (E. coli) / References: UniProt: C7G6F8
#2: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpb1-4DManpb1-4DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a1122h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpb1-4DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1122h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.38 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M ammonium acetate, 0.1 M 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: 0.97625 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: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.4→48.57 Å / Num. obs: 61043 / % possible obs: 98.7 % / Redundancy: 3.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.097 / Net I/σ(I): 8.2
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 2 / Num. unique obs: 8942 / CC1/2: 0.713 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
PHASERphasing
SCALAdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HFZ

6hfz


Resolution: 2.4→47.84 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.913 / SU B: 10.06 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.511 / ESU R Free: 0.285 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25331 3029 5 %RANDOM
Rwork0.18057 ---
obs0.18406 57988 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.77 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å20 Å20.74 Å2
2--0.25 Å20 Å2
3---0.35 Å2
Refinement stepCycle: 1 / Resolution: 2.4→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11568 0 147 487 12202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01411987
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710523
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.67116285
X-RAY DIFFRACTIONr_angle_other_deg0.8141.65524696
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.05651459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05423.296631
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.171151957
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1671556
X-RAY DIFFRACTIONr_chiral_restr0.0540.21616
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213371
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022213
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_it3.0965.0945860
X-RAY DIFFRACTIONr_mcbond_other3.0915.0945859
X-RAY DIFFRACTIONr_mcangle_it4.6237.6317311
X-RAY DIFFRACTIONr_mcangle_other4.6237.6327312
X-RAY DIFFRACTIONr_scbond_it3.2265.4076127
X-RAY DIFFRACTIONr_scbond_other3.2235.4076127
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9367.9898975
X-RAY DIFFRACTIONr_long_range_B_refined7.26359.25713305
X-RAY DIFFRACTIONr_long_range_B_other7.25659.25413242
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 258 -
Rwork0.27 4251 -
obs--99.14 %

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