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- PDB-4qk0: Crystal structure of Ara127N-Se, a GH127 beta-L-arabinofuranosida... -

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Basic information

Entry
Database: PDB / ID: 4qk0
TitleCrystal structure of Ara127N-Se, a GH127 beta-L-arabinofuranosidase from Geobacillus Stearothermophilus T6
ComponentsGH127 beta-L-arabinofuranoside
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
Glycoside hydrolase family 127 protein
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.258 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 Ara127N-Se, 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 / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GH127 beta-L-arabinofuranoside
B: GH127 beta-L-arabinofuranoside
C: GH127 beta-L-arabinofuranoside
D: GH127 beta-L-arabinofuranoside


Theoretical massNumber of molelcules
Total (without water)301,0484
Polymers301,0484
Non-polymers00
Water27,3471518
1
A: GH127 beta-L-arabinofuranoside
B: GH127 beta-L-arabinofuranoside


Theoretical massNumber of molelcules
Total (without water)150,5242
Polymers150,5242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-24 kcal/mol
Surface area45510 Å2
MethodPISA
2
C: GH127 beta-L-arabinofuranoside
D: GH127 beta-L-arabinofuranoside


Theoretical massNumber of molelcules
Total (without water)150,5242
Polymers150,5242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-22 kcal/mol
Surface area45500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.383, 132.266, 109.045
Angle α, β, γ (deg.)90.00, 113.06, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 8 - 642 / Label seq-ID: 14 - 648

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 75261.891 Da / Num. of mol.: 4
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1518 / 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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG3350, 1% Tryptone, 0.1 M HEPES sodium, pH 7, 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: Apr 28, 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: 2.258→40 Å / Num. all: 122372 / Num. obs: 121797 / % possible obs: 99.53 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 6.7
Reflection shellResolution: 2.258→2.29 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 3.2 / % possible all: 94.23

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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: 2.258→40 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.142 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.297 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20048 6452 5 %RANDOM
Rwork0.15748 ---
all0.15965 122372 --
obs0.15965 121797 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.756 Å2
Baniso -1Baniso -2Baniso -3
1--2.02 Å20 Å2-1.47 Å2
2--1.2 Å2-0 Å2
3---1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.258→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20588 0 0 1518 22106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01921216
X-RAY DIFFRACTIONr_bond_other_d0.0080.0219737
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.95628801
X-RAY DIFFRACTIONr_angle_other_deg1.28345343
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15752562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24823.6931094
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.21153331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.56215161
X-RAY DIFFRACTIONr_chiral_restr0.1030.22981
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02124296
X-RAY DIFFRACTIONr_gen_planes_other0.0070.025165
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_it3.2223.210182
X-RAY DIFFRACTIONr_mcbond_other3.2183.210181
X-RAY DIFFRACTIONr_mcangle_it4.8134.78912727
X-RAY DIFFRACTIONr_mcangle_other4.8134.78912728
X-RAY DIFFRACTIONr_scbond_it4.1953.64511034
X-RAY DIFFRACTIONr_scbond_other4.1953.64611035
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5185.28916062
X-RAY DIFFRACTIONr_long_range_B_refined8.74826.59225907
X-RAY DIFFRACTIONr_long_range_B_other8.726.46525374
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A401400.07
12B401400.07
21A402080.07
22C402080.07
31A401130.07
32D401130.07
41B402020.08
42C402020.08
51B401090.08
52D401090.08
61C402290.08
62D402290.08
LS refinement shellResolution: 2.258→2.317 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 443 -
Rwork0.204 8583 -
obs--94.23 %

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