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- PDB-7nde: Trichoderma parareesei PL7A beta-glucuronan lyase -

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Basic information

Entry
Database: PDB / ID: 7nde
TitleTrichoderma parareesei PL7A beta-glucuronan lyase
ComponentsGlucuronan lyase
KeywordsLYASE / glucuronan lyase / b-jelly roll
Function / homologyAlginate lyase 2 / Alginate lyase / Concanavalin A-like lectin/glucanase domain superfamily / lyase activity / Alginate lyase
Function and homology information
Biological speciesTrichoderma parareesei (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsFredslund, F. / Welner, D.H. / Wilkens, C.
CitationJournal: Chem.Commun.(Camb.) / Year: 2024
Title: Glucuronan lyases from family PL7 use a Tyr/Tyr syn beta-elimination catalytic mechanism for glucuronan breakdown.
Authors: Vuillemin, M. / Pilgaard, B. / Kiehn, E. / Fredslund, F. / Welner, D.H. / Meyer, A.S. / Aachmann, F.L. / Wilkens, C.
History
DepositionFeb 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucuronan lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9983
Polymers25,7141
Non-polymers2832
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint6 kcal/mol
Surface area10090 Å2
Unit cell
Length a, b, c (Å)69.589, 69.589, 111.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-421-

HOH

21A-581-

HOH

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Components

#1: Protein Glucuronan lyase


Mass: 25714.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoderma parareesei (fungus) / Gene: A9Z42_0012760 / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A2H2ZFD4
#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.: 1 / Source method: obtained synthetically / 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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4 M disodium malonate pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.45→43.55 Å / Num. obs: 49303 / % possible obs: 99.98 % / Redundancy: 26.2 % / Biso Wilson estimate: 23.37 Å2 / CC1/2: 1 / Net I/σ(I): 22.47
Reflection shellResolution: 1.45→1.5 Å / Num. unique obs: 4791 / CC1/2: 0.44

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
XDSdata scaling
Cootmodel building
PHASERphasing
PHENIX1.18refinement
PHENIX1.18refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CWS

2cws


Resolution: 1.45→43.55 Å / SU ML: 0.136 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.4812
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1738 1982 4.27 %
Rwork0.1548 44448 -
obs0.1556 46430 93.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.68 Å2
Refinement stepCycle: LAST / Resolution: 1.45→43.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1722 0 18 186 1926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00761907
X-RAY DIFFRACTIONf_angle_d0.9852620
X-RAY DIFFRACTIONf_chiral_restr0.0821297
X-RAY DIFFRACTIONf_plane_restr0.0071350
X-RAY DIFFRACTIONf_dihedral_angle_d16.4565677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.480.34341190.33352495X-RAY DIFFRACTION75.57
1.48-1.520.27351220.27872703X-RAY DIFFRACTION81.6
1.52-1.570.28121290.24162876X-RAY DIFFRACTION86.18
1.57-1.620.21911310.21552979X-RAY DIFFRACTION88.91
1.62-1.680.21691340.19083066X-RAY DIFFRACTION92.3
1.68-1.750.20341390.17843170X-RAY DIFFRACTION94.54
1.75-1.820.18931460.15753239X-RAY DIFFRACTION96.52
1.82-1.920.15221460.14493280X-RAY DIFFRACTION98.03
1.92-2.040.15841470.14073331X-RAY DIFFRACTION98.69
2.04-2.20.15571500.13923369X-RAY DIFFRACTION99.77
2.2-2.420.17561500.13683388X-RAY DIFFRACTION99.89
2.42-2.770.19581530.15213427X-RAY DIFFRACTION99.97
2.77-3.490.1671540.15523479X-RAY DIFFRACTION100
3.49-43.550.15731620.1473646X-RAY DIFFRACTION99.92
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)
17.96830968322-1.223735472045.614920013240.767454228895-1.663250438627.538512037930.0840184829533-0.4954093329020.006151229620560.09195295233790.05992926268090.003845574908710.202975469203-0.230374121235-0.09359647465740.24831894935-0.0292980385133-0.0087738724920.2824450172650.05069490518260.1997693463422.948390725942.913603372261.4796262615
25.63070322181-1.00229001919-1.219901668885.047957727820.1222009758086.100054135550.09024166096610.21490089205-0.476724073974-0.239931403206-0.02029320710870.2742104973440.528314954551-0.486412093141-0.08117901066010.289168910087-0.0822999354836-0.04689592685450.2086898734980.04500021625930.24048132835718.820090451835.230691594351.5005027185
32.60533352511-0.5225282541-0.2954855476721.62509201291-0.1999804844480.972331174230.1161857626850.236640948904-0.0674147015022-0.165071388257-0.04646718466910.01118427831850.125689866271-0.161743256119-0.08207488335640.275080708199-0.0198869775056-0.0179585058650.2754745319830.03562413439930.20719892875624.277970014242.605656975545.6677077215
42.94374330212-0.3743624546840.2853834680331.38734966467-0.09130848479990.9653115867980.0494772525174-0.2275068063340.105720123036-0.0004420171636830.01724834820170.0564735813790.0319578239598-0.14007747621-0.06240372460380.209955562132-0.01447841032370.00497914518910.2512023808580.0439914626360.16381462586117.372638820152.117787958649.8372074171
56.4238301487-0.9504787554122.094467223621.77103673129-0.4953403021811.824698917470.01142976005380.1798459085550.282077330947-0.104303923463-0.00440439814212-0.00972347918453-0.0296022957959-0.0707891371456-0.01155104470030.229601434576-0.005255433398080.01271201970570.2382637121710.05572728771860.19314821908521.363577902357.505713973542.1206534126
64.58873169282-0.4507247323691.418880546780.81516851054-0.6430963387211.51190298585-0.166989315773-0.1549430501870.3519127581320.03860685003790.056167313095-0.0583416765075-0.110704717186-0.117112815950.1327301825820.234686228310.000459484819912-0.0128011430590.2023729502560.004349358141340.24835217887918.317762627162.16650818948.0123687594
74.16533062337-1.84384422984-1.351906639921.871620251760.4774385758972.058124497340.1092597643440.3904075347670.133551634105-0.244779810852-0.112883044114-0.09020660437570.0593505851456-0.0830200020878-0.02809582375990.23841988887-0.0176306709965-0.00857281595020.2619766537320.05053783056670.18664805878122.490584566548.708600639342.7757353006
85.75640744015-1.5262597377-1.791457860182.607557123420.2704839805094.30237423487-0.0899144396509-0.4115852941330.09618238705540.241500155550.114251164332-0.01334170477690.0833298254287-0.167163464355-0.0436721685980.204132238025-0.0325832764192-0.01202596871080.2653467460350.03750866843920.15736368021221.646381885551.42173213256.6751210771
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 39 )-1 - 391 - 21
22chain 'A' and (resid 40 through 66 )40 - 6622 - 48
33chain 'A' and (resid 67 through 104 )67 - 10449 - 89
44chain 'A' and (resid 105 through 149 )105 - 14990 - 141
55chain 'A' and (resid 150 through 169 )150 - 169142 - 166
66chain 'A' and (resid 170 through 221 )170 - 221167 - 226
77chain 'A' and (resid 222 through 237 )222 - 237227 - 242
88chain 'A' and (resid 238 through 251 )238 - 251243 - 258

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