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- PDB-6rtv: Crystal Structure of Glucuronoyl Esterase from Cerrena unicolor i... -

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Basic information

Entry
Database: PDB / ID: 6rtv
TitleCrystal Structure of Glucuronoyl Esterase from Cerrena unicolor inactive S270A variant
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 / 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
4-O-methyl-glucuronoyl methylesterase
Similarity search - Component
Biological speciesCerrena unicolor (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.46 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

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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)87,65614
Polymers86,4222
Non-polymers1,23412
Water13,637757
1
A: 4-O-methyl-glucuronoyl methylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7706
Polymers43,2111
Non-polymers5605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 4-O-methyl-glucuronoyl methylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8868
Polymers43,2111
Non-polymers6757
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.273, 84.273, 261.127
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-898-

HOH

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Components

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Protein / Sugars , 2 types, 4 molecules AB

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


Mass: 43210.930 Da / Num. of mol.: 2 / Fragment: catalytic domain / Mutation: S270A
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
#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 / 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

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Non-polymers , 4 types, 767 molecules

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


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


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 757 / 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: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7, 0.1 M KCl, 25% w/v SOKALAN CP7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.46→49.17 Å / Num. obs: 163708 / % possible obs: 100 % / Redundancy: 9.7 % / Biso Wilson estimate: 11.52 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.053 / Rrim(I) all: 0.167 / Net I/σ(I): 7.5 / Num. measured all: 1584810 / Scaling rejects: 256
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
1.46-1.487.80.8646192979460.4550.3240.9261.899.3
7.99-49.178.20.038986012070.9990.0140.04118.999.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.3data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PIC

3pic


Resolution: 1.46→44.392 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.79
RfactorNum. reflection% reflection
Rfree0.1994 8194 5.01 %
Rwork0.1822 --
obs0.183 163459 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 68.96 Å2 / Biso mean: 15.2268 Å2 / Biso min: 6.63 Å2
Refinement stepCycle: final / Resolution: 1.46→44.392 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5818 0 147 757 6722
Biso mean--30.19 24.7 -
Num. residues----772
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.46-1.47660.29222800.288751235403
1.4766-1.4940.30032880.271950795367
1.494-1.51220.28492750.261550885363
1.5122-1.53130.2792760.250551165392
1.5313-1.55150.26352620.238750855347
1.5515-1.57270.24862760.227751135389
1.5727-1.59520.23422610.220751445405
1.5952-1.6190.22232760.210750735349
1.619-1.64430.23632510.207751505401
1.6443-1.67130.26512760.218450985374
1.6713-1.70010.25112860.213751055391
1.7001-1.7310.21132780.201451415419
1.731-1.76430.22362600.19651345394
1.7643-1.80030.20542690.197251385407
1.8003-1.83950.20812610.18951465407
1.8395-1.88230.19372470.184151645411
1.8823-1.92930.21292830.183151275410
1.9293-1.98150.20522770.186851305407
1.9815-2.03980.22262830.180551465429
2.0398-2.10570.2082680.188851775445
2.1057-2.18090.18212650.165751535418
2.1809-2.26820.20712680.179652075475
2.2682-2.37150.1832760.17651755451
2.3715-2.49650.18972800.172252025482
2.4965-2.65290.18182620.170452465508
2.6529-2.85770.19092660.172852295495
2.8577-3.14520.19032980.176352555553
3.1452-3.60010.182660.163252955561
3.6001-4.5350.14372770.142153815658
4.535-44.41260.17013030.15756455948
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)
12.14460.3345-0.02571.9418-0.61572.15780.0242-0.23810.04490.2125-0.01270.0376-0.0617-0.0737-0.04150.1052-0.0068-0.01920.0881-0.02030.082265.510347.983331.2723
20.3367-0.1024-0.04920.39250.02480.2945-0.00160.0141-0.01480.0072-0.0020.0684-0.0049-0.01920.00450.11310.0052-0.00420.0757-0.00170.097245.393748.500915.4202
30.32120.0966-0.02630.5525-0.18640.48720.01650.0178-0.0267-0.0171-0.03470.00570.01370.01150.020.10210.0123-0.00640.0833-0.00530.09359.523640.663213.0068
40.71510.3948-0.06090.587-0.01680.5110.0151-0.0112-0.11430.0123-0.0175-0.03230.0230.06890.01510.12410.0225-0.00320.08580.010.111764.862831.942615.7426
52.58470.2419-0.81581.74040.05743.60830.061-0.24390.23130.2055-0.02260.0212-0.2143-0.0849-0.03980.11840.0003-0.03010.0991-0.02360.12944.15917.555736.0393
61.2706-0.41960.30560.5556-0.03510.6194-0.0067-0.0484-0.01930.0627-0.00690.0805-0.0222-0.07260.0130.08840.00320.0160.0703-0.01510.105326.46410.279927.9169
71.08960.36090.39657.19583.99453.9062-0.003-0.00720.041-0.31470.08530.004-0.2545-0.0958-0.04780.08560.02540.00960.1139-0.00020.125211.929417.029119.2578
81.297-0.293-0.62430.8872-0.04592.4116-0.05990.0351-0.13050.0277-0.0510.23830.2038-0.27330.05780.0966-0.02480.00430.1147-0.02840.156112.0833-1.960918.6389
90.52350.0084-0.07850.542-0.01730.38150.00650.04660.0377-0.0084-0.01230.0354-0.0225-0.02290.00610.09620.0028-0.00190.0802-0.00120.089231.12266.678517.0615
101.01660.1419-0.18980.58360.10560.95170.00280.0018-0.08450.0196-0.01970.04710.0906-0.01080.01970.10970.00190.00050.0573-0.00050.106534.0833-10.207521.0011
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 73 through 128 )A73 - 128
2X-RAY DIFFRACTION2chain 'A' and (resid 129 through 317 )A129 - 317
3X-RAY DIFFRACTION3chain 'A' and (resid 318 through 422 )A318 - 422
4X-RAY DIFFRACTION4chain 'A' and (resid 423 through 458 )A423 - 458
5X-RAY DIFFRACTION5chain 'B' and (resid 73 through 110 )B73 - 110
6X-RAY DIFFRACTION6chain 'B' and (resid 111 through 149 )B111 - 149
7X-RAY DIFFRACTION7chain 'B' and (resid 150 through 172 )B150 - 172
8X-RAY DIFFRACTION8chain 'B' and (resid 173 through 205 )B173 - 205
9X-RAY DIFFRACTION9chain 'B' and (resid 206 through 370 )B206 - 370
10X-RAY DIFFRACTION10chain 'B' and (resid 371 through 458 )B371 - 458

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