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- PDB-8b8e: Wild-type GH11 from Blastobotrys mokoenaii -

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Basic information

Entry
Database: PDB / ID: 8b8e
TitleWild-type GH11 from Blastobotrys mokoenaii
ComponentsBmGH11
KeywordsCARBOHYDRATE / endo-b-1 / 4-xylanase / xylan / b-jelly roll
Function / homologyTRIS-HYDROXYMETHYL-METHYL-AMMONIUM / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION
Function and homology information
Biological speciesBlastobotrys mokoenaii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsColeman, T. / Ravn, J.L. / Larsbrink, J.
Funding support Sweden, European Union, 3items
OrganizationGrant numberCountry
Carl Trygger FoundationCTS 19:195 Sweden
Carl Trygger FoundationCTS 18:118 Sweden
European Union (EU)964430European Union
CitationJournal: Microbiol Spectr / Year: 2023
Title: Yeasts Have Evolved Divergent Enzyme Strategies To Deconstruct and Metabolize Xylan.
Authors: Ravn, J.L. / Ristinmaa, A.S. / Coleman, T. / Larsbrink, J. / Geijer, C.
History
DepositionOct 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BmGH11
B: BmGH11
C: BmGH11
D: BmGH11
E: BmGH11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,72940
Polymers121,2155
Non-polymers2,51435
Water13,169731
1
A: BmGH11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,95711
Polymers24,2431
Non-polymers71410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BmGH11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,11112
Polymers24,2431
Non-polymers86811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: BmGH11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5976
Polymers24,2431
Non-polymers3545
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: BmGH11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3844
Polymers24,2431
Non-polymers1413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: BmGH11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6807
Polymers24,2431
Non-polymers4376
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.039, 37.860, 142.609
Angle α, β, γ (deg.)90.000, 104.270, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
BmGH11


Mass: 24242.996 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blastobotrys mokoenaii (fungus) / Production host: Komagataella pastoris (fungus) / References: endo-1,4-beta-xylanase

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Non-polymers , 8 types, 766 molecules

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


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 731 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: JCSG+ kit condition D12: 0.04 M Potassium phosphate monobasic, 16 % w/v PEG 8000, 20% w/v glycerol; 32.5 mg/mL BmGH11. 3 weeks at room temperature.
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→80.48 Å / Num. obs: 125550 / % possible obs: 99.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 18.25 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.083 / Rrim(I) all: 0.154 / Net I/σ(I): 4.3 / Num. measured all: 412389 / Scaling rejects: 1868
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
1.55-1.582.71.091588559220.3690.7731.3450.894.9
8.48-80.4830.06926038740.9770.0450.083999.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.55 Å80.48 Å
Translation1.55 Å80.48 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2 model of BmGH11

Resolution: 1.55→63.11 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2252 1998 1.6 %Random selection, 5% reflections
Rwork0.193 122812 --
obs0.1935 124810 98.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.78 Å2 / Biso mean: 23.5248 Å2 / Biso min: 9.53 Å2
Refinement stepCycle: final / Resolution: 1.55→63.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7295 0 376 731 8402
Biso mean--39.84 31.17 -
Num. residues----957
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.590.35871350.3558260839594
1.59-1.630.33541480.32358675882398
1.63-1.680.33271360.30458642877899
1.68-1.730.29661470.2728704885199
1.73-1.790.30011430.24748698884199
1.79-1.870.26191320.22998756888899
1.87-1.950.26021460.22298748889499
1.95-2.050.22821410.18187688909100
2.05-2.180.23191410.179588588999100
2.18-2.350.19551450.173388268971100
2.35-2.590.21011430.17788794893799
2.59-2.960.21841440.173989319075100
2.96-3.730.18511480.159189509098100
3.73-63.110.20451490.17992029351100

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