[English] 日本語
Yorodumi
- PDB-6rv8: Crystal Structure of Glucuronoyl Esterase from Cerrena unicolor c... -

+
Open data


ID or keywords:

Loading...

-
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 / cellulose binding / carboxylic ester hydrolase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function
: / Glucuronyl esterase, fungi / 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 ...: / Glucuronyl esterase, fungi / 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
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
1
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

-
Components

-
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

-
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


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


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

-
Non-polymers , 2 types, 580 molecules

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


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


Mass: 18.015 Da / Num. of mol.: 579 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more