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- PDB-6rv8: Crystal Structure of Glucuronoyl Esterase from Cerrena unicolor c... -

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Basic information

Entry
Database: PDB / ID: 6rv8
TitleCrystal Structure of Glucuronoyl Esterase from Cerrena unicolor covalent complex with the aldouronic acid UXXR
Components4-O-methyl-glucuronoyl methylesterase
KeywordsHYDROLASE / CE15 / esterase / alpha/beta-hydrolase / ligand-bound
Function / homology
Function and homology information


(4-O-methyl)-D-glucuronate-lignin esterase / lignin catabolic process / carboxylic ester hydrolase activity / cellulose binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4beta-beta-xylobiose / alpha-D-mannopyranose / 4-O-methyl-glucuronoyl methylesterase
Similarity search - Component
Biological speciesCerrena unicolor (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
Model detailsS270A variant in complex with the aldouronic acid Um4X
AuthorsErnst, H.A. / Mosbech, C. / Langkilde, A. / Westh, P. / Meyer, A. / Agger, J.W. / Larsen, S.
CitationJournal: Nat Commun / Year: 2020
Title: The structural basis of fungal glucuronoyl esterase activity on natural substrates.
Authors: Ernst, H.A. / Mosbech, C. / Langkilde, A.E. / Westh, P. / Meyer, A.S. / Agger, J.W. / Larsen, S.
History
DepositionMay 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 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: 4-O-methyl-glucuronoyl methylesterase
B: 4-O-methyl-glucuronoyl methylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,99911
Polymers101,8852
Non-polymers2,1149
Water10,431579
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A: 4-O-methyl-glucuronoyl methylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8686
Polymers50,9431
Non-polymers9265
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 4-O-methyl-glucuronoyl methylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1315
Polymers50,9431
Non-polymers1,1884
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.750, 84.750, 261.062
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-850-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 4-O-methyl-glucuronoyl methylesterase / Glucuronoyl esterase / GE


Mass: 50942.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cerrena unicolor (fungus) / Plasmid: pPICZ-alpha / Production host: Komagataella pastoris (fungus) / Variant (production host): X-33
References: UniProt: A0A0A7EQR3, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases

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Sugars , 4 types, 8 molecules

#2: Polysaccharide 4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-Xylitol


Type: oligosaccharide / Mass: 606.526 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,4,3/[h212h][a212h-1b_1-5][a2122A-1a_1-5_4*OC]/1-2-2-3/a4-b1_b4-c1_c2-d1WURCSPDB2Glycan 1.1.0
[][<C5O4>]{[(1+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(2+1)][a-D-Glcp4Me]{}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 282.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-xylobiose
DescriptorTypeProgram
DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a212h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 580 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 579 / 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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M ammonium acetate, 0.1 M bis-tris pH 5.5, 17% w/v PEG10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.8→44.45 Å / Num. obs: 85042 / % possible obs: 95.5 % / Redundancy: 24.2 % / Biso Wilson estimate: 24.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.021 / Rrim(I) all: 0.103 / Net I/σ(I): 24 / Num. measured all: 2056826 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.8317.71.1585527131310.7620.2721.1932.767.9
9.52-44.4520.10.0351498974710.0080.03662.699.3

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.3data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RTV

6rtv


Resolution: 1.85→44.45 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.69
RfactorNum. reflection% reflection
Rfree0.181 3997 4.98 %
Rwork0.1494 --
obs0.1509 80245 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.98 Å2 / Biso mean: 27.3344 Å2 / Biso min: 14.17 Å2
Refinement stepCycle: final / Resolution: 1.85→44.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5740 0 240 579 6559
Biso mean--53.98 34.16 -
Num. residues----762
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.87180.2555910.21882025211676
1.8718-1.89460.24011140.1962166228082
1.8946-1.91860.191150.1912372248789
1.9186-1.94380.23861520.18442505265796
1.9438-1.97050.2111350.16592621275697
1.9705-1.99860.21551360.15452553268998
1.9986-2.02840.19561420.15082623276599
2.0284-2.06010.20871500.15322616276699
2.0601-2.09390.21541400.15032620276099
2.0939-2.130.19151370.1462659279699
2.13-2.16870.17581300.14822632276299
2.1687-2.21050.161270.14272665279299
2.2105-2.25560.17611500.15212652280299
2.2556-2.30460.17121460.148726422788100
2.3046-2.35820.17891270.151126742801100
2.3582-2.41720.17331440.146426452789100
2.4172-2.48250.18851380.151726692807100
2.4825-2.55560.19531380.148326762814100
2.5556-2.63810.19971350.153626852820100
2.6381-2.73230.18881420.155527022844100
2.7323-2.84170.19511360.158626752811100
2.8417-2.9710.1981390.167326892828100
2.971-3.12760.19641610.1626932854100
3.1276-3.32350.18161380.162227302868100
3.3235-3.580.18821430.152327282871100
3.58-3.94010.17681270.136427682895100
3.9401-4.50980.15361550.123227592914100
4.5098-5.680.13771560.12828152971100
5.68-44.46620.17251530.152429893142100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.75320.4448-0.80924.0153-0.11412.87370.0833-0.44350.12170.2185-0.101-0.0968-0.21920.00320.00150.2648-0.0288-0.05280.2607-0.00470.167370.272749.488826.9122
22.51690.14320.2912.29790.21561.4882-0.0155-0.2589-0.03230.24290.0424-0.0803-0.0146-0.06640.00060.2167-0.0123-0.01420.1763-0.01390.161663.891544.595230.7042
30.484-0.1754-0.00860.88140.02690.4341-0.00080.0051-0.03540.064-0.01810.191-0.0051-0.06020.01640.222-0.00280.00760.1591-0.00530.191745.3747.658515.8531
40.56820.03980.01190.3264-0.2840.81150.00980.0337-0.0770.0287-0.0321-0.01680.05450.02250.02310.21280.0068-0.00360.1471-0.00480.18859.413439.948412.7079
50.57220.32350.09860.6935-0.16960.5512-0.0123-0.0297-0.14110.0617-0.0228-0.0090.12240.06110.06150.24670.02620.0020.1430.00080.222364.551631.244516.4809
62.91950.1984-1.00464.29540.39093.229-0.1081-0.47570.31870.08550.0328-0.0996-0.32450.00010.02620.26190.0155-0.06640.2764-0.06390.222547.29577.06431.0683
72.4753-0.32720.62991.2392-0.30930.8354-0.0856-0.2720.14940.19560.0680.0837-0.1716-0.26890.00820.22840.0350.02140.2347-0.05510.187931.0257.204931.6415
81.5523-0.7315-0.49961.35270.1942.4651-0.01350.03390.13190.04740.01040.2774-0.0418-0.43980.04090.17950.0341-0.00220.3635-0.00930.295812.35154.132421.3053
91.54860.4418-0.17171.63690.68331.6830.01870.08470.2579-0.13960.00080.2784-0.3413-0.28540.00020.28430.0711-0.05050.23050.00630.316226.279517.629614.878
102.7126-0.4042-0.38211.0876-0.05750.7728-0.0688-0.11550.02960.09080.05730.1988-0.0606-0.19130.01210.18360.01590.00170.196-0.00490.183728.19892.448320.5607
110.82270.02050.25480.91820.14081.2409-0.0187-0.01210.0160.0264-0.03170.0504-0.0143-0.0910.0450.17370.0060.00430.1553-0.01220.17336.9343-1.637418.5214
122.6888-0.58820.24322.58530.31152.1725-0.0131-0.211-0.3580.11070.00570.24180.381-0.32170.04740.2374-0.07590.04030.30620.01580.356322.23-14.963924.2545
131.0510.01250.34611.13460.21832.1082-0.0099-0.0256-0.03230.05250.0267-0.0480.09640.0508-0.01390.18480.0133-0.00730.14120.00820.165244.579-10.64923.2071
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 80 through 99 )A80 - 99
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 128 )A100 - 128
3X-RAY DIFFRACTION3chain 'A' and (resid 129 through 317 )A129 - 317
4X-RAY DIFFRACTION4chain 'A' and (resid 318 through 422 )A318 - 422
5X-RAY DIFFRACTION5chain 'A' and (resid 423 through 460 )A423 - 460
6X-RAY DIFFRACTION6chain 'B' and (resid 80 through 99 )B80 - 99
7X-RAY DIFFRACTION7chain 'B' and (resid 100 through 149 )B100 - 149
8X-RAY DIFFRACTION8chain 'B' and (resid 150 through 205 )B150 - 205
9X-RAY DIFFRACTION9chain 'B' and (resid 206 through 235 )B206 - 235
10X-RAY DIFFRACTION10chain 'B' and (resid 236 through 317 )B236 - 317
11X-RAY DIFFRACTION11chain 'B' and (resid 318 through 408 )B318 - 408
12X-RAY DIFFRACTION12chain 'B' and (resid 409 through 432 )B409 - 432
13X-RAY DIFFRACTION13chain 'B' and (resid 433 through 460 )B433 - 460

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