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- PDB-8u49: The Apo Crystal Structure of BlCel9A from Glycoside Hydrolase Family 9 -

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Basic information

Entry
Database: PDB / ID: 8u49
TitleThe Apo Crystal Structure of BlCel9A from Glycoside Hydrolase Family 9
ComponentsEndoglucanase
KeywordsHYDROLASE / Cellulase / GH9 / Bacillus licheniformis
Function / homology
Function and homology information


cellulose binding / cellulase / cellulase activity / cellulose catabolic process
Similarity search - Function
Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily / CBM3 (carbohydrate binding type-3) domain profile. / Glycoside hydrolase family 9 ...Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily / CBM3 (carbohydrate binding type-3) domain profile. / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / CBM2/CBM3, carbohydrate-binding domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
Biological speciesBacillus licheniformis DSM 13 = ATCC 14580 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAraujo, E.A. / Polikarpov, I.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)158752/2015-5 Brazil
Sao Paulo Research Foundation (FAPESP)2021/08780-1 Brazil
CitationJournal: Carbohydr Polym / Year: 2024
Title: Molecular mechanism of cellulose depolymerization by the two-domain BlCel9A enzyme from the glycoside hydrolase family 9.
Authors: de Araujo, E.A. / Cortez, A.A. / Pellegrini, V.O.A. / Vacilotto, M.M. / Cruz, A.F. / Batista, P.R. / Polikarpov, I.
History
DepositionSep 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,54412
Polymers69,8511
Non-polymers69311
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-24 kcal/mol
Surface area23050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.571, 67.406, 100.916
Angle α, β, γ (deg.)90.000, 125.060, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-1200-

HOH

21A-1219-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Endoglucanase


Mass: 69850.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis DSM 13 = ATCC 14580 (bacteria)
Strain: ATCC 14580 / Gene: celA, BL01232 / Plasmid: pETTrx-1a/LIC / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q65JI9, cellulase

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Non-polymers , 7 types, 432 molecules

#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 6 mg/mL protein, 100 mM Tris, pH 8.5, 15% w/v PEG20000, crystal growth within ~5 days

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45866 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45866 Å / Relative weight: 1
ReflectionResolution: 1.8→36.87 Å / Num. obs: 66792 / % possible obs: 97.6 % / Redundancy: 5.7 % / Biso Wilson estimate: 21.06 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.1825 / Rpim(I) all: 0.08224 / Rrim(I) all: 0.2009 / Net I/av σ(I): 0.82 / Net I/σ(I): 9.26
Reflection shellResolution: 1.8→5.38 Å / Mean I/σ(I) obs: 9.31 / Num. unique obs: 66792 / CC1/2: 0.99 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JS4

1js4


Resolution: 1.8→36.87 Å / SU ML: 0.2461 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.379
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2067 3338 5 %
Rwork0.1726 63404 -
obs0.1743 66742 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.58 Å2
Refinement stepCycle: LAST / Resolution: 1.8→36.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4921 0 40 421 5382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00565174
X-RAY DIFFRACTIONf_angle_d0.79397042
X-RAY DIFFRACTIONf_chiral_restr0.0462696
X-RAY DIFFRACTIONf_plane_restr0.0071924
X-RAY DIFFRACTIONf_dihedral_angle_d12.76881841
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.4161170.39862227X-RAY DIFFRACTION82.68
1.83-1.850.3611290.34312450X-RAY DIFFRACTION93.75
1.85-1.880.3471380.3082625X-RAY DIFFRACTION97.19
1.88-1.910.31241390.27352629X-RAY DIFFRACTION97.91
1.91-1.950.29461360.26632598X-RAY DIFFRACTION97.78
1.95-1.980.29161370.27372594X-RAY DIFFRACTION95.76
1.98-2.020.2951380.2492614X-RAY DIFFRACTION97.9
2.02-2.060.26491380.19742628X-RAY DIFFRACTION99.6
2.06-2.110.22171420.1942695X-RAY DIFFRACTION99.68
2.11-2.160.27071390.17992648X-RAY DIFFRACTION99.71
2.16-2.210.24081420.17332684X-RAY DIFFRACTION99.75
2.21-2.270.23461390.17442658X-RAY DIFFRACTION99.89
2.27-2.340.20781440.16582731X-RAY DIFFRACTION99.93
2.34-2.410.21261410.162666X-RAY DIFFRACTION99.96
2.41-2.50.19651400.16692667X-RAY DIFFRACTION99.89
2.5-2.60.24091400.1742667X-RAY DIFFRACTION99.75
2.6-2.720.17181420.16452693X-RAY DIFFRACTION99.89
2.72-2.860.18741410.16692672X-RAY DIFFRACTION99.75
2.86-3.040.21141420.17312704X-RAY DIFFRACTION99.72
3.04-3.270.20131410.16442687X-RAY DIFFRACTION99.4
3.27-3.60.16211410.15262672X-RAY DIFFRACTION99.29
3.6-4.120.16631410.13362676X-RAY DIFFRACTION99.12
4.12-5.190.14641440.11922728X-RAY DIFFRACTION99.86
5.19-36.870.15721470.14392791X-RAY DIFFRACTION99.86
Refinement TLS params.Method: refined / Origin x: 31.152936933 Å / Origin y: -0.869924039897 Å / Origin z: 21.1024305213 Å
111213212223313233
T0.174257126718 Å2-0.00595862416876 Å2-0.0094293131399 Å2-0.157880105458 Å2-0.0134280156117 Å2--0.191057757144 Å2
L0.202806108676 °20.0384654600129 °2-0.194306873142 °2-0.231478336355 °2-0.238920858816 °2--0.723519810374 °2
S0.0138251456387 Å °0.000975134595573 Å °0.0148069748198 Å °-0.0169634853286 Å °-0.0203708432568 Å °-0.0107524432712 Å °0.0223118623339 Å °-0.00709100898075 Å °0.00666476918062 Å °
Refinement TLS groupSelection details: all

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