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- PDB-6k9d: glycoside hydrolase family 12 (GH12) englucanase -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6k9d
Titleglycoside hydrolase family 12 (GH12) englucanase
ComponentsGH12 beta-1, 4-endoglucanase
KeywordsHYDROLASE / endoglucanase / beta-jelly-roll
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: 1.505 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 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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: GH12 beta-1, 4-endoglucanase


Theoretical massNumber of molelcules
Total (without water)24,1831
Polymers24,1831
Non-polymers00
Water4,504250
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9110 Å2
Unit cell
Length a, b, c (Å)88.631, 88.631, 123.411
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-470-

HOH

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Components

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


Mass: 24183.301 Da / Num. of mol.: 1 / Mutation: N18Y
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.: 250 / 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: 5.01 Å3/Da / Density % sol: 75.45 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: NfEG12A-N18Y was concentrated to 10 mg/ml in a buffer containing 100 mM citric acid-Na2HPO4 (pH 7.2). both proteins were crystallized in a mother liquid with 0.1 M citrate (pH 5.0) and 16% ...Details: NfEG12A-N18Y was concentrated to 10 mg/ml in a buffer containing 100 mM citric acid-Na2HPO4 (pH 7.2). both proteins were 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-N18Y 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: 100 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: 1.505→55.879 Å / Num. obs: 62640 / % possible obs: 79.95 % / Redundancy: 4.3 % / Net I/σ(I): 1.34
Reflection shellResolution: 1.5048→4.2789 Å / Num. unique obs: 23

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
Cootmodel building
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.505→55.879 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.79
RfactorNum. reflection% reflection
Rfree0.1862 3181 5.08 %
Rwork0.1732 --
obs0.1738 62640 79.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.505→55.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1709 0 0 250 1959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061844
X-RAY DIFFRACTIONf_angle_d0.8062544
X-RAY DIFFRACTIONf_dihedral_angle_d5.6241380
X-RAY DIFFRACTIONf_chiral_restr0.056273
X-RAY DIFFRACTIONf_plane_restr0.005327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5048-1.52730.353160.243985X-RAY DIFFRACTION3
1.5273-1.55120.3263210.2604273X-RAY DIFFRACTION9
1.5512-1.57660.2976210.2435546X-RAY DIFFRACTION17
1.5766-1.60380.3148320.2758879X-RAY DIFFRACTION27
1.6038-1.63290.2935560.27161274X-RAY DIFFRACTION40
1.6329-1.66430.3112880.2631817X-RAY DIFFRACTION57
1.6643-1.69830.29011410.26212644X-RAY DIFFRACTION83
1.6983-1.73530.25521610.26233156X-RAY DIFFRACTION98
1.7353-1.77560.26561800.24833179X-RAY DIFFRACTION100
1.7756-1.820.241740.22853206X-RAY DIFFRACTION100
1.82-1.86920.22081610.22133206X-RAY DIFFRACTION100
1.8692-1.92420.18921870.19533195X-RAY DIFFRACTION100
1.9242-1.98640.2091760.18033184X-RAY DIFFRACTION100
1.9864-2.05740.19341680.17593227X-RAY DIFFRACTION100
2.0574-2.13970.19851720.17173231X-RAY DIFFRACTION100
2.1397-2.23710.18641920.1733198X-RAY DIFFRACTION100
2.2371-2.35510.19551860.16923217X-RAY DIFFRACTION100
2.3551-2.50260.18511720.18833245X-RAY DIFFRACTION100
2.5026-2.69580.21871880.1853253X-RAY DIFFRACTION100
2.6958-2.96710.21081860.18583255X-RAY DIFFRACTION100
2.9671-3.39640.1771720.16383315X-RAY DIFFRACTION100
3.3964-4.27890.13531480.13433360X-RAY DIFFRACTION100
4.2789-55.81760.15391930.15593514X-RAY DIFFRACTION100

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