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- PDB-6ru2: Crystal Structure of Glucuronoyl Esterase from Cerrena unicolor -

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Basic information

Entry
Database: PDB / ID: 6ru2
TitleCrystal Structure of Glucuronoyl Esterase from Cerrena unicolor
Components4-O-methyl-glucuronoyl methylesterase
KeywordsHYDROLASE / CE15 / esterase / alpha/beta-hydrolase
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
alpha-D-mannopyranose / 4-O-methyl-glucuronoyl methylesterase
Similarity search - Component
Biological speciesCerrena unicolor (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
Model detailsApo-form
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 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr2_auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)88,05712
Polymers86,6542
Non-polymers1,40210
Water9,764542
1
A: 4-O-methyl-glucuronoyl methylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9715
Polymers43,3271
Non-polymers6444
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 4-O-methyl-glucuronoyl methylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0867
Polymers43,3271
Non-polymers7596
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.450, 84.450, 262.239
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-835-

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: 43327.121 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 , 2 types, 6 molecules

#2: 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
#3: 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

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Non-polymers , 4 types, 546 molecules

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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M ammonium acetate, 0.1 M bis-tris pH 5.5, 17% PEG10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.91837 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91837 Å / Relative weight: 1
ReflectionResolution: 1.96→49.31 Å / Num. obs: 68208 / % possible obs: 98.9 % / Redundancy: 8.7 % / Biso Wilson estimate: 20.05 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.261 / Rpim(I) all: 0.092 / Rrim(I) all: 0.278 / Net I/σ(I): 5.8 / Num. measured all: 590244 / Scaling rejects: 70
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
1.96-2.018.31.1833682044220.6780.431.2611.697.8
9.19-49.317.20.08157677970.9970.030.08714.399.2

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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: 1.96→44.554 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.78
RfactorNum. reflection% reflection
Rfree0.2041 3380 4.97 %
Rwork0.1778 --
obs0.1791 67955 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.64 Å2 / Biso mean: 21.243 Å2 / Biso min: 11.55 Å2
Refinement stepCycle: final / Resolution: 1.96→44.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5714 0 151 542 6407
Biso mean--46.08 26.67 -
Num. residues----758
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.96-1.9880.29731330.25952576270996
1.988-2.01770.25871380.25142621275998
2.0177-2.04920.30561460.23162615276197
2.0492-2.08280.27751490.22772581273098
2.0828-2.11870.2451350.22122668280398
2.1187-2.15720.25051290.20942631276098
2.1572-2.19870.22251320.20882643277598
2.1987-2.24360.26391370.20922657279498
2.2436-2.29240.24451370.19892651278898
2.2924-2.34570.22921340.19992665279998
2.3457-2.40440.21771530.19072625277898
2.4044-2.46940.20061290.18492653278298
2.4694-2.5420.22411450.18152660280598
2.542-2.62410.23741280.18592690281898
2.6241-2.71790.1941390.17852682282198
2.7179-2.82670.23571350.18772687282299
2.8267-2.95530.20591420.19192692283499
2.9553-3.1110.20751650.18852702286799
3.111-3.30590.19991360.17982727286399
3.3059-3.56110.17971450.16992753289899
3.5611-3.91920.19921280.15192759288799
3.9192-4.48590.14051500.1282801295199
4.4859-5.64990.1581590.130328312990100
5.6499-44.5660.16221560.15913005316199
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)
12.35680.9823-0.89733.5366-0.72822.5509-0.0917-0.31510.0930.1561-0.0748-0.25-0.13760.14220.1080.2013-0.0091-0.08240.1694-0.02930.140328.31887.277526.9803
22.91391.03870.05312.1789-0.03392.70760.0533-0.297-0.05320.184-0.0684-0.12140.0791-0.06830.02530.1552-0.0053-0.00760.1386-0.01450.136421.65473.246431.1821
30.6695-0.0554-0.12750.6698-0.03820.3486-0.00880.0212-0.02790.04250.00260.1067-0.0203-0.0390.00290.19280.0086-0.00990.12580.00040.13463.13126.218615.6706
40.5626-0.1331-0.07660.2768-0.25461.01070.00530.0407-0.034-0.0229-0.052-0.0367-0.07070.0670.05350.19480.0034-0.00640.1319-0.00140.141919.90515.961312.7563
50.52570.2249-0.01930.36920.12351.6008-0.0377-0.0006-0.08610.0074-0.0621-0.00430.04110.03980.09110.18520.019-0.00950.1373-0.00910.17817.7724-8.173913.5124
62.1481-0.1566-0.35962.0311-0.14212.33050.05390.0024-0.2646-0.00460.0156-0.02540.15680.0265-0.0670.217-0.0056-0.020.1321-0.03190.21566.1915-15.453715.3465
70.67170.30110.61941.4121-0.53442.49910.10990.0022-0.13380.0164-0.0189-0.1260.14940.2494-0.09790.16430.0378-0.01030.12630.00490.162828.3763-8.036515.4737
82.31390.9967-0.91052.0161-0.96892.50840.0508-0.27110.06070.0718-0.0801-0.0636-0.11750.13880.00990.1855-0.0173-0.04090.1746-0.03150.14684.7133-35.003930.6828
92.15520.2832-0.07471.4412-0.41792.3394-0.0059-0.19990.03770.2361-0.0543-0.0488-0.05240.0120.04890.19170.0040.00080.1567-0.03130.1829-2.4141-37.067135.4362
102.3739-0.29460.06150.7054-0.09050.8205-0.0042-0.1194-0.11120.0802-0.03620.1511-0.0764-0.16390.0270.20.00570.04180.1839-0.01740.2496-26.6653-28.86623.2246
111.3641-0.85380.24582.17321.27172.43670.0163-0.03890.2285-0.1225-0.01980.1066-0.1553-0.1466-0.00820.18430.02420.02490.2018-0.02620.2489-30.3871-25.802419.5481
121.9494-0.416-1.0151.5723-0.09352.7307-0.09330.0992-0.05060.0296-0.00160.30880.1967-0.51350.05320.1525-0.0530.00620.2293-0.02720.2152-30.0207-44.39418.8972
131.27420.62250.08481.6430.52661.47210.03980.09860.152-0.08720.04840.2008-0.1794-0.0572-0.09190.19520.0241-0.00010.15760.01360.2196-15.8012-23.469913.7832
141.430.255-0.2310.91890.00550.7573-0.0172-0.0183-0.00420.0139-0.03610.0707-0.0125-0.03140.04880.16580.00160.00010.1312-0.00410.1436-11.501-36.595118.0252
150.64040.3279-0.02940.51480.14820.80530.0020.0098-0.03070.0473-0.03570.05650.0337-0.03130.04240.17420.003-0.00510.13540.0020.1698-6.8458-47.128819.3826
163.3201-0.8733-0.52823.18631.41542.9874-0.1205-0.0566-0.40310.2788-0.15690.21950.4499-0.20180.25930.2037-0.04740.03620.1460.00660.2582-20.6075-55.961922.8998
171.05680.1781-0.01991.44260.50023.86460.0417-0.0193-0.08540.05220.0117-0.13180.2210.2321-0.0410.17520.0138-0.02540.10980.01210.17462.5292-51.981422.0977
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 81 through 100 )A81 - 100
2X-RAY DIFFRACTION2chain 'A' and (resid 101 through 128 )A101 - 128
3X-RAY DIFFRACTION3chain 'A' and (resid 129 through 317 )A129 - 317
4X-RAY DIFFRACTION4chain 'A' and (resid 318 through 370 )A318 - 370
5X-RAY DIFFRACTION5chain 'A' and (resid 371 through 408 )A371 - 408
6X-RAY DIFFRACTION6chain 'A' and (resid 409 through 432 )A409 - 432
7X-RAY DIFFRACTION7chain 'A' and (resid 433 through 459 )A433 - 459
8X-RAY DIFFRACTION8chain 'B' and (resid 81 through 100 )B81 - 100
9X-RAY DIFFRACTION9chain 'B' and (resid 101 through 128 )B101 - 128
10X-RAY DIFFRACTION10chain 'B' and (resid 129 through 149 )B129 - 149
11X-RAY DIFFRACTION11chain 'B' and (resid 150 through 172 )B150 - 172
12X-RAY DIFFRACTION12chain 'B' and (resid 173 through 205 )B173 - 205
13X-RAY DIFFRACTION13chain 'B' and (resid 206 through 235 )B206 - 235
14X-RAY DIFFRACTION14chain 'B' and (resid 236 through 338 )B236 - 338
15X-RAY DIFFRACTION15chain 'B' and (resid 339 through 408 )B339 - 408
16X-RAY DIFFRACTION16chain 'B' and (resid 409 through 432 )B409 - 432
17X-RAY DIFFRACTION17chain 'B' and (resid 433 through 459 )B433 - 459

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