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- PDB-4kcb: Crystal Structure of Exo-1,5-alpha-L-arabinanase from Bovine Rumi... -

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Basic information

Entry
Database: PDB / ID: 4kcb
TitleCrystal Structure of Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library
ComponentsArabinan endo-1,5-alpha-L-arabinosidase
KeywordsHYDROLASE / beta-propeller / GH43 / glycoside hydrolase / arabinanase
Function / homology
Function and homology information


arabinan endo-1,5-alpha-L-arabinosidase activity / arabinan catabolic process
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
PHOSPHATE ION / Exo-alpha-1,5-L-arabinanase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSantos, C.R. / Polo, C.C. / Costa, M.C.M.F. / Nascimento, A.F.Z. / Wong, D.W.S. / Murakami, M.T.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Mechanistic strategies for catalysis adopted by evolutionary distinct family 43 arabinanases.
Authors: Santos, C.R. / Polo, C.C. / Costa, M.C. / Nascimento, A.F. / Meza, A.N. / Cota, J. / Hoffmam, Z.B. / Honorato, R.V. / Oliveira, P.S. / Goldman, G.H. / Gilbert, H.J. / Prade, R.A. / Ruller, R. ...Authors: Santos, C.R. / Polo, C.C. / Costa, M.C. / Nascimento, A.F. / Meza, A.N. / Cota, J. / Hoffmam, Z.B. / Honorato, R.V. / Oliveira, P.S. / Goldman, G.H. / Gilbert, H.J. / Prade, R.A. / Ruller, R. / Squina, F.M. / Wong, D.W. / Murakami, M.T.
History
DepositionApr 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arabinan endo-1,5-alpha-L-arabinosidase
B: Arabinan endo-1,5-alpha-L-arabinosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,9265
Polymers100,6412
Non-polymers2853
Water34219
1
A: Arabinan endo-1,5-alpha-L-arabinosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4152
Polymers50,3201
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Arabinan endo-1,5-alpha-L-arabinosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5103
Polymers50,3201
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)140.115, 140.115, 159.011
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Detailsthe biological unit is a monomer; there are 2 biological units in asymmetric unit

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Components

#1: Protein Arabinan endo-1,5-alpha-L-arabinosidase


Mass: 50320.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Description: THE SAMPLE SEQUENCE WAS IDENTIFIED FROM A DNA LIBRARY CONSTRUCTED FROM BOVINE RUMEN FLUID (WONG ET AL., 2008)
Production host: Escherichia coli (E. coli)
References: UniProt: D2XML8, arabinan endo-1,5-alpha-L-arabinanase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Ammonium Phosphate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2013
RadiationMonochromator: Si(111)double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 20619 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.9→3 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→35.03 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.885 / SU B: 15.203 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.396 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26656 1055 5.1 %RANDOM
Rwork0.21709 ---
obs0.21962 19562 97.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.944 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.03 Å20 Å2
2--0.07 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.9→35.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4864 0 15 19 4898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225023
X-RAY DIFFRACTIONr_angle_refined_deg1.1251.9216807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7535603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55923.81252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.62815791
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0261529
X-RAY DIFFRACTIONr_chiral_restr0.0850.2653
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213968
X-RAY DIFFRACTIONr_mcbond_it0.4551.53002
X-RAY DIFFRACTIONr_mcangle_it0.85624797
X-RAY DIFFRACTIONr_scbond_it0.8532021
X-RAY DIFFRACTIONr_scangle_it1.4914.52010
LS refinement shellResolution: 2.896→2.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 91 -
Rwork0.289 1402 -
obs--99.4 %

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