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- PDB-1ks5: Structure of Aspergillus niger endoglucanase -

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Basic information

Entry
Database: PDB / ID: 1ks5
TitleStructure of Aspergillus niger endoglucanase
ComponentsEndoglucanase A
KeywordsHYDROLASE / Aspergillus niger / Endoglucanase / Cellulase / Jelly-roll / familly 12 / glycosyl hydrolase
Function / homology
Function and homology information


cellulase / cellulase activity / polysaccharide catabolic process / transferase activity / extracellular region
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
Acetyltransferase (GNAT) family protein
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKhademi, S. / Zhang, D. / Swanson, S.M. / Wartenberg, A. / Witte, C. / Meyer, E.F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Determination of the structure of an endoglucanase from Aspergillus niger and its mode of inhibition by palladium chloride.
Authors: Khademi, S. / Zhang, D. / Swanson, S.M. / Wartenberg, A. / Witte, K. / Meyer, E.F.
History
DepositionJan 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Remark 650HELIX AUTHOR PROVIDED HELIX RECORDS
Remark 700SHEET AUTHOR PROVIDED SHEET RECORDS

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoglucanase A


Theoretical massNumber of molelcules
Total (without water)24,2831
Polymers24,2831
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.57, 131.57, 71.64
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Endoglucanase A


Mass: 24283.145 Da / Num. of mol.: 1 / Fragment: Catalytic Domain / Source method: isolated from a natural source / Source: (natural) Aspergillus niger (mold) / Strain: CBS 554.65 / References: UniProt: O74705, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O

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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: 3.19 Å3/Da / Density % sol: 61.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: PEG 4000, Sodium Acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19 mg/mlprotein1drop
228 %PEG40001reservoir
3100 mMacetate1reservoirpH4.8

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAC Science DIP-2030K / Detector: IMAGE PLATE / Date: Oct 1, 1994 / Details: mirrors
RadiationMonochromator: osmic, Model 140-000023 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. all: 18707 / Num. obs: 18194 / % possible obs: 97.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.07
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.3 / % possible all: 95.5
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 18660 / % possible obs: 98 % / Num. measured all: 325097
Reflection shell
*PLUS
% possible obs: 95.5 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 6.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.191 1789 RANDOM
Rwork0.175 --
all-18707 -
obs-18194 -
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1717 0 0 125 1842
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_improper_angle_d0.62
LS refinement shellResolution: 2.1→2.18 Å / Rfactor Rfree error: 0.016
RfactorNum. reflection% reflection
Rfree0.199 156 -
Rwork0.185 --
obs-1729 94.2 %
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.34
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.62

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