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- PDB-3d5y: High resolution crystal structure of 1,5-alpha-arabinanase cataly... -

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Basic information

Entry
Database: PDB / ID: 3d5y
TitleHigh resolution crystal structure of 1,5-alpha-arabinanase catalytic mutant (AbnBE201A)
ComponentsIntracellular arabinanase
KeywordsHYDROLASE / Arabinanase / Glycosyl Hydrolase / High resolution / 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 / SYNCHROTRON / AB INITIO / Resolution: 1.22 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 1.2Nov 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 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)35,5862
Polymers35,5461
Non-polymers401
Water5,008278
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)71,1714
Polymers71,0912
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2450 Å2
ΔGint-37 kcal/mol
Surface area24320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.854, 89.672, 75.503
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: 35545.527 Da / Num. of mol.: 1 / Mutation: E201A
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.: 278 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE 9TH RESIDUE, GLY, IS NOT A PLANNED MUTATION BUT A MUTATION IN THE CURRENT MODELS.

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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: 39.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.9M lithium sulfate, 0.1M Tris buffer pH 8.5, 4%(w/v) PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978578 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 26, 2005
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978578 Å / Relative weight: 1
ReflectionResolution: 1.22→50 Å / Num. all: 86543 / Num. obs: 83088 / % possible obs: 96 % / Redundancy: 16 % / Biso Wilson estimate: 11.1 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.059 / Net I/σ(I): 16.6
Reflection shellResolution: 1.22→1.24 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.24 / Num. unique all: 3707 / Rsym value: 0.268

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO
Starting model: PDB ENTRY 3CU9

3cu9


Resolution: 1.22→30 Å / Num. parameters: 21381 / Num. restraintsaints: 26021 / Isotropic thermal model: Anisotropic / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.1923 4150 5.3 %RANDOM
all0.158 78902 --
obs0.1581 78902 90.1 %-
Displacement parametersBiso mean: 17.8 Å2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2797.5
FreeObs
Luzzati coordinate error0.14 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.22→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2516 0 1 278 2795
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0318
X-RAY DIFFRACTIONs_zero_chiral_vol0.074
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.082
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.027
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.046
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 1.22→1.3 Å / Rfactor Rfree error: 0.007
RfactorNum. reflection% reflection
Rfree0.245 1216 -
Rwork0.24 --
obs--86.1 %

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