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- PDB-3d60: Crystal Structure Analysis of 1,5-alpha-arabinanase catalytic mut... -

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Basic information

Entry
Database: PDB / ID: 3d60
TitleCrystal Structure Analysis of 1,5-alpha-arabinanase catalytic mutant (D27A)
ComponentsIntracellular arabinanase
KeywordsHYDROLASE / Arabinanase / Glycosyl Hydrolase / beta-propeller / Geobacillus stearothermophilus
Function / homology
Function and homology information


arabinan endo-1,5-alpha-L-arabinanase / arabinan endo-1,5-alpha-L-arabinosidase activity / arabinan catabolic process / metal ion binding / cytoplasm
Similarity search - Function
Glycoside hydrolase, family 43, endo-1, 5-alpha-L-arabinosidase / : / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Mainly Beta
Similarity search - Domain/homology
Intracellular endo-alpha-(1->5)-L-arabinanase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAlhassid, A. / Ben David, A. / Shoham, Y. / Shoham, G.
CitationJournal: Biochem.J. / Year: 2009
Title: Crystal structure of an inverting GH 43 1,5-alpha-L-arabinanase from Geobacillus stearothermophilus complexed with its substrate
Authors: Alhassid, A. / Ben-David, A. / Tabachnikov, O. / Libster, D. / Naveh, E. / Zolotnitsky, G. / Shoham, Y. / Shoham, G.
History
DepositionMay 18, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 6, 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: Intracellular arabinanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6572
Polymers35,6171
Non-polymers401
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Intracellular arabinanase
hetero molecules

A: Intracellular arabinanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3134
Polymers71,2332
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2590 Å2
ΔGint-34 kcal/mol
Surface area24560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.507, 89.745, 75.622
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Intracellular arabinanase / 1 / 5-alpha-arabinanase


Mass: 35616.605 Da / Num. of mol.: 1 / Mutation: D27A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Strain: T-6 / Gene: abn / Plasmid: pET9d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B3EYM8, arabinan endo-1,5-alpha-L-arabinanase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.04 Å3/Da / Density % sol: 39.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.75M lithium sulfate, 0.1M Tris buffer pH 8.5, 3% (w/v) PGME 2000, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 19, 2006
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 24489 / Num. obs: 23506 / % possible obs: 96 % / Observed criterion σ(F): 1 / Redundancy: 7.1 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.055 / Net I/σ(I): 14
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.36 / Num. unique all: 1121 / Rsym value: 0.406 / % possible all: 93.1

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Processing

Software
NameVersionClassification
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CU9

3cu9


Resolution: 1.9→28.92 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 480062.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2205 10 %RANDOM
Rwork0.193 ---
obs0.193 22094 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.5155 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 22.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20 Å2
2---3.47 Å20 Å2
3---2.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.9→28.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2521 0 1 201 2723
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it2.92.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.273 319 9.3 %
Rwork0.239 3114 -
obs--90.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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