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- PDB-3cu9: High resolution crystal structure of 1,5-alpha-L-arabinanase from... -

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Basic information

Entry
Database: PDB / ID: 3cu9
TitleHigh resolution crystal structure of 1,5-alpha-L-arabinanase from Geobacillus Stearothermophilus
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: 1.06 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
DepositionApr 16, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 9, 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)35,7933
Polymers35,6611
Non-polymers1322
Water7,170398
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)71,5866
Polymers71,3212
Non-polymers2644
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3020 Å2
ΔGint-38 kcal/mol
Surface area24360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.141, 89.579, 76.041
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1094-

HOH

21A-1187-

HOH

31A-1328-

HOH

41A-1371-

HOH

51A-1402-

HOH

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Components

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


Mass: 35660.613 Da / Num. of mol.: 1
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.06 Å3/Da / Density % sol: 40.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.7M Lithium Sulfate, 0.1M Tris buffer pH 7.5, 15% (v/v) Glycerol, 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 27, 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: 1.06→50 Å / Num. all: 132831 / Num. obs: 130844 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.6 % / Biso Wilson estimate: 6.1 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 16.7
Reflection shellResolution: 1.06→1.08 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.258 / Rsym value: 0.235 / % possible all: 77.7

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO
Starting model: PDB ENTRY 1WL7

1wl7


Resolution: 1.06→30 Å / Num. parameters: 22516 / Num. restraintsaints: 27102 / 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
Rfree0.1761 6547 5.3 %RANDOM
Rwork0.1472 ---
all0.1475 124263 --
obs0.1472 124263 93.4 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 14.5 Å2
Refine analyzeNum. disordered residues: 396 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2926.7
FreeObs
Luzzati coordinate error0.11 Å0.11 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.06→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2523 0 7 398 2928
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0338
X-RAY DIFFRACTIONs_zero_chiral_vol0.093
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.095
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.033
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.039
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 1.06→1.13 Å / Rfactor Rfree error: 0.007
RfactorNum. reflection% reflection
Rfree0.3 2017 -
Rwork0.297 --
obs--89.6 %

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