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- PDB-4qjy: Crystal structure of native Ara127N, a GH127 beta-L-arabinofurano... -

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Basic information

Entry
Database: PDB / ID: 4qjy
TitleCrystal structure of native Ara127N, a GH127 beta-L-arabinofuranosidase from Geobacillus Stearothermophilus T6
ComponentsGH127 beta-L-arabinofuranosidase
KeywordsHYDROLASE / glycoside hydrolase
Function / homology
Function and homology information


carbohydrate metabolic process
Similarity search - Function
: / : / Glycoside hydrolase family 127 C-terminal domain / Beta-L-arabinofuranosidase, GH127 / : / Beta-L-arabinofuranosidase, GH127 catalytic domain / Beta-L-arabinofuranosidase, GH127 middle domain / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
ACETATE ION / Glycoside hydrolase family 127 protein
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.294 Å
AuthorsLansky, S. / Salama, R. / Dann, R. / Shner, I. / Manjasetty, B. / Belrhali, H. / Shoham, Y. / Shoham, G.
CitationJournal: To be Published
Title: Crystal structure of native Ara127N, a GH127 beta-L-arabinofuranosidase from Geobacillus Stearothermophilus T6
Authors: Lansky, S. / Salama, R. / Dann, R. / Shner, I. / Manjasetty, B. / Belrhali, H. / Shoham, Y. / Shoham, G.
History
DepositionJun 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GH127 beta-L-arabinofuranosidase
B: GH127 beta-L-arabinofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,76613
Polymers149,1172
Non-polymers64911
Water10,881604
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-25 kcal/mol
Surface area45640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.536, 118.098, 174.984
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GH127 beta-L-arabinofuranosidase / Ara127N


Mass: 74558.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Strain: T6 / Gene: araN / Production host: Escherichia coli (E. coli) / References: UniProt: B3EYN9
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / 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: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% PEG300, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 8, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.294→30 Å / Num. all: 58582 / Num. obs: 58318 / % possible obs: 99.55 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 8.5
Reflection shellResolution: 2.294→2.34 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 2.4 / % possible all: 98.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
AutoSolphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.294→29.89 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.946 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.308 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2141 3118 5.1 %RANDOM
Rwork0.15012 ---
obs0.15337 58318 99.55 %-
all-58582 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.825 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å2-0 Å2
2---2.68 Å20 Å2
3---3.21 Å2
Refinement stepCycle: LAST / Resolution: 2.294→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10318 0 44 604 10966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01910679
X-RAY DIFFRACTIONr_bond_other_d0.0010.029919
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.9514495
X-RAY DIFFRACTIONr_angle_other_deg0.855322779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.99451284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97723.688545
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.898151753
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0061580
X-RAY DIFFRACTIONr_chiral_restr0.1020.21498
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02112236
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022580
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8623.2355135
X-RAY DIFFRACTIONr_mcbond_other2.8573.235123
X-RAY DIFFRACTIONr_mcangle_it4.3994.8396406
X-RAY DIFFRACTIONr_mcangle_other4.3994.8396407
X-RAY DIFFRACTIONr_scbond_it3.6143.6275544
X-RAY DIFFRACTIONr_scbond_other3.6143.6275545
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6785.2828084
X-RAY DIFFRACTIONr_long_range_B_refined7.83126.37912796
X-RAY DIFFRACTIONr_long_range_B_other7.83126.38212797
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.294→2.353 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 218 -
Rwork0.205 4117 -
obs--96.03 %

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