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- PDB-6k98: Substrates promiscuity of xyloglucanases and endoglucanases of gl... -

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Basic information

Entry
Database: PDB / ID: 6k98
TitleSubstrates promiscuity of xyloglucanases and endoglucanases of glycoside hydrolase 12 family
ComponentsGH12 beta-1, 4-endoglucanase
KeywordsHYDROLASE / endoglucanase / glycoside hydrolase family 12 / PROTEIN FIBRIL
Function / homology
Function and homology information


cellulase / cellulase activity / polysaccharide catabolic process
Similarity search - Function
Glycoside hydrolase family 12 / Glycosyl hydrolase family 12 / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
GH12 beta-1, 4-endoglucanase
Similarity search - Component
Biological speciesAspergillus fischeri (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.032 Å
AuthorsHong, Y. / Tao, T. / Pengjun, S. / Jiaming, C. / Xiaoyu, W. / Chen, H. / yingguo, B. / Bin, Y.
CitationJournal: To Be Published
Title: Substrates promiscuity of xyloglucanases and endoglucanases of glycoside hydrolase 12 family
Authors: Hong, Y. / Tao, T. / Pengjun, S. / Jiaming, C. / Xiaoyu, W. / Chen, H. / yingguo, B. / Bin, Y.
History
DepositionJun 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 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: GH12 beta-1, 4-endoglucanase


Theoretical massNumber of molelcules
Total (without water)24,2051
Polymers24,2051
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8940 Å2
Unit cell
Length a, b, c (Å)92.708, 92.708, 119.928
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein GH12 beta-1, 4-endoglucanase / glycoside hydrolase family 12 endoglucanase


Mass: 24205.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fischeri (mold) / Gene: Nfeg12A / Variant: CGMCC 3.15369 / Production host: Komagataella phaffii CBS 7435 (fungus) / References: UniProt: A0A1L6CE30, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 5.32 Å3/Da / Density % sol: 76.89 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: NfEG12A was concentrated to 10 mg/ml in a buffer containing 100 mM citric acid-Na2HPO4 (pH 7.2). The protein was crystallized in a mother liquid with 0.1 M citrate (pH 5.0) and 16% (w/v) PEG ...Details: NfEG12A was concentrated to 10 mg/ml in a buffer containing 100 mM citric acid-Na2HPO4 (pH 7.2). The protein was crystallized in a mother liquid with 0.1 M citrate (pH 5.0) and 16% (w/v) PEG 20000 using the hanging drop vapor diffusion method in 24-well plates. NfEG12A crystals was transferred to a reservoir solution supplemented with 25% (v/v) ethylene glycol to grown. Obtained crystals were cryoprotected with 25% (v/v) 2-methyl-2,4-pentanediol. The crystals were mounted on a nylon loop and cooled immediately in liquid nitrogen prior to data collection.

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1.00919 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00919 Å / Relative weight: 1
ReflectionResolution: 2.032→57.522 Å / Num. obs: 29949 / % possible obs: 87.23 % / Redundancy: 4.2 % / Net I/σ(I): 1.35
Reflection shellResolution: 2.03255→4.519 Å / Num. unique obs: 11

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KS4

1ks4


Resolution: 2.032→57.522 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.74
RfactorNum. reflection% reflection
Rfree0.212 1491 4.98 %
Rwork0.1853 --
obs0.1866 29949 87.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.032→57.522 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1710 0 0 80 1790
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071800
X-RAY DIFFRACTIONf_angle_d0.8392470
X-RAY DIFFRACTIONf_dihedral_angle_d5.8761351
X-RAY DIFFRACTIONf_chiral_restr0.055264
X-RAY DIFFRACTIONf_plane_restr0.005316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0325-2.09810.3087340.308638X-RAY DIFFRACTION22
2.0981-2.17310.35321190.30262052X-RAY DIFFRACTION71
2.1731-2.26010.2908940.30352056X-RAY DIFFRACTION69
2.2601-2.36290.33191490.27862878X-RAY DIFFRACTION99
2.3629-2.48750.27811590.27642923X-RAY DIFFRACTION100
2.4875-2.64340.29841730.25082912X-RAY DIFFRACTION100
2.6434-2.84740.28431430.24462959X-RAY DIFFRACTION100
2.8474-3.1340.25151670.22372944X-RAY DIFFRACTION100
3.134-3.58740.21171590.19212978X-RAY DIFFRACTION100
3.5874-4.51950.16081430.14422920X-RAY DIFFRACTION96
4.5195-57.54490.16861510.14233198X-RAY DIFFRACTION100

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