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- PDB-1ks4: The structure of Aspergillus niger endoglucanase-palladium complex -

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Basic information

Entry
Database: PDB / ID: 1ks4
TitleThe structure of Aspergillus niger endoglucanase-palladium complex
ComponentsEndoglucanase A
KeywordsHYDROLASE / Endoglucanase / Cellulase / Aspergillus niger / family 9 / (alpha/alpha)6
Function / homology
Function and homology information


cellulase / cellulase activity / polysaccharide catabolic process / transferase activity
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
PALLADIUM ION / Acetyltransferase (GNAT) family protein
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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

Downloads & links

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Assembly

Deposited unit
A: Endoglucanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6024
Polymers24,2831
Non-polymers3193
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.088, 131.088, 71.985
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: Aspergillus niger Endoglucanase / Source method: isolated from a natural source / Source: (natural) Aspergillus niger (mold) / Strain: CBS 554.65 / References: UniProt: O74705, cellulase
#2: Chemical ChemComp-PD / PALLADIUM ION / Palladium


Mass: 106.420 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Pd
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.18 Å3/Da / Density % sol: 61.36 %
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: 2.5→30 Å / Num. all: 11142 / Num. obs: 10691 / % possible obs: 96 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 26.7
Reflection shellResolution: 2.5→2.55 Å / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 3.7 / % possible all: 89.5
Reflection
*PLUS
Num. obs: 11084 / Num. measured all: 117527 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
Highest resolution: 2.5 Å / % possible obs: 89.3 % / Rmerge(I) obs: 0.63

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30 Å / Rfactor Rfree error: 0.007 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1104 10.3 %RANDOM
Rwork0.214 ---
all0.218 11142 --
obs0.218 10691 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.743 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso mean: 43.4 Å2
Baniso -1Baniso -2Baniso -3
1--5.03 Å20 Å20 Å2
2---5.03 Å20 Å2
3---10.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1717 0 3 34 1754
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d27
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it1.761.5
X-RAY DIFFRACTIONc_mcangle_it3.172
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it3.212.5
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.339 100 10.3 %
Rwork0.296 871 -
obs-971 90 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top
Refinement
*PLUS
Rfactor Rfree: 0.242 / Rfactor Rwork: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.43
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7

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