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- PDB-7wvr: Crystal structure of Talaromyces leycettanus JCM12802 expansin -

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Basic information

Entry
Database: PDB / ID: 7wvr
TitleCrystal structure of Talaromyces leycettanus JCM12802 expansin
ComponentsEXLX1
KeywordsSUGAR BINDING PROTEIN / Talaromyces leycettanus JCM12802 / Expansin-like protein
Function / homology
Function and homology information


anatomical structure morphogenesis
Similarity search - Function
: / : / Expansin/pollen allergen, DPBB domain / Expansin, family-45 endoglucanase-like domain profile. / RlpA-like protein, double-psi beta-barrel domain / Lytic transglycolase / Expansin, cellulose-binding-like domain superfamily / RlpA-like domain superfamily
Similarity search - Domain/homology
Biological speciesEvansstolkia leycettana (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsDing, S.J. / Luo, H.Y. / Yao, B. / Tu, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Bioresour Technol / Year: 2022
Title: Boosting enzymatic degradation of cellulose using a fungal expansin: Structural insight into the pretreatment mechanism
Authors: Ding, S. / Liu, X. / Hakulinen, N. / Taherzadeh, M.J. / Wang, Y. / Wang, Y. / Qin, X. / Wang, X. / Yao, B. / Luo, H. / Tu, T.
History
DepositionFeb 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EXLX1


Theoretical massNumber of molelcules
Total (without water)20,8341
Polymers20,8341
Non-polymers00
Water5,423301
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8720 Å2
Unit cell
Length a, b, c (Å)47.862, 117.627, 99.203
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-476-

HOH

21A-695-

HOH

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Components

#1: Protein EXLX1


Mass: 20833.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Evansstolkia leycettana (fungus) / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A3G6JEW6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
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: 3.35 Å3/Da / Density % sol: 63.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.8 M ammonium sulfate, 0.1 M Bis-Tris (pH 6.5), and 2% PEG monomethyl ether 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.407→25.3 Å / Num. obs: 50454 / % possible obs: 92.32 % / Redundancy: 2 % / Biso Wilson estimate: 16.36 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.48
Reflection shellResolution: 1.407→1.457 Å / Rmerge(I) obs: 0.3292 / Mean I/σ(I) obs: 2.34 / Num. unique obs: 3433 / CC1/2: 0.785 / Rrim(I) all: 0.4656

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JCW

4jcw


Resolution: 1.41→25.3 Å / SU ML: 0.1383 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.6472 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1756 2501 4.96 %
Rwork0.1614 47943 -
obs0.1622 50444 92.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.18 Å2
Refinement stepCycle: LAST / Resolution: 1.41→25.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1462 0 0 301 1763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00551585
X-RAY DIFFRACTIONf_angle_d0.79222187
X-RAY DIFFRACTIONf_chiral_restr0.0868252
X-RAY DIFFRACTIONf_plane_restr0.0048286
X-RAY DIFFRACTIONf_dihedral_angle_d3.4651805
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.430.3522760.29591729X-RAY DIFFRACTION60.57
1.43-1.460.2665930.26511974X-RAY DIFFRACTION69.41
1.46-1.50.2861320.25082407X-RAY DIFFRACTION84.02
1.5-1.530.26571220.21822713X-RAY DIFFRACTION94.66
1.53-1.570.18141480.18142707X-RAY DIFFRACTION94.91
1.57-1.610.19511300.18552722X-RAY DIFFRACTION95.23
1.61-1.660.20851330.18472764X-RAY DIFFRACTION95.74
1.66-1.710.20681350.17242783X-RAY DIFFRACTION96.49
1.71-1.770.22161650.1722731X-RAY DIFFRACTION96.73
1.77-1.840.18611430.16342786X-RAY DIFFRACTION96.99
1.84-1.930.17851700.15772771X-RAY DIFFRACTION97.09
1.93-2.030.19871510.15452794X-RAY DIFFRACTION97.23
2.03-2.160.17191390.14812833X-RAY DIFFRACTION97.96
2.16-2.320.16971700.15642794X-RAY DIFFRACTION98.05
2.32-2.560.16621500.15412877X-RAY DIFFRACTION98.38
2.56-2.930.18961470.15932876X-RAY DIFFRACTION98.89
2.93-3.680.15481300.14982680X-RAY DIFFRACTION90.12
Refinement TLS params.Method: refined / Origin x: -20.6141377159 Å / Origin y: -17.8141460123 Å / Origin z: -3.18276678162 Å
111213212223313233
T0.113303668801 Å20.00126404065063 Å20.0136994704853 Å2-0.133995672698 Å2-0.00135351395728 Å2--0.124586189877 Å2
L0.427780386087 °2-0.168952819255 °20.129556068249 °2-1.28756642039 °2-0.434059285882 °2--0.659496129252 °2
S0.00208643167193 Å °-0.00114315182452 Å °-0.0343711962681 Å °-0.0158841379431 Å °0.00374203668892 Å °0.0170594639943 Å °-0.0415019561226 Å °0.000397865573343 Å °-0.00682007932562 Å °
Refinement TLS groupSelection details: all

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