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- PDB-5xfm: Crystal structure of beta-arabinopyranosidase -

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Basic information

Entry
Database: PDB / ID: 5xfm
TitleCrystal structure of beta-arabinopyranosidase
ComponentsAlpha-glucosidase
KeywordsHYDROLASE / Arabinopyranosidase
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / metabolic process / carbohydrate binding
Similarity search - Function
Glycosyl-hydrolase 97, catalytic domain / Glycosyl-hydrolase 97, C-terminal oligomerisation domain / Glycosyl-hydrolase 97, N-terminal domain / Glycoside hydrolase 97 / Glycosyl-hydrolase 97 N-terminal / Glycosyl-hydrolase 97 C-terminal, oligomerisation / Glycoside hydrolase-type carbohydrate-binding / Glycosyl hydrolase, all-beta / Aldolase-type TIM barrel / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Glycoside hydrolase family 97 protein / Alpha-glucosidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKato, K. / Okuyama, M. / Yao, M.
CitationJournal: Biochimie / Year: 2017
Title: A novel glycoside hydrolase family 97 enzyme: Bifunctional beta-l-arabinopyranosidase/ alpha-galactosidase from Bacteroides thetaiotaomicron.
Authors: Kikuchi, A. / Okuyama, M. / Kato, K. / Osaki, S. / Ma, M. / Kumagai, Y. / Matsunaga, K. / Klahan, P. / Tagami, T. / Yao, M. / Kimura, A.
History
DepositionApr 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-glucosidase
B: Alpha-glucosidase
C: Alpha-glucosidase
D: Alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)293,0118
Polymers292,8514
Non-polymers1604
Water22,6451257
1
A: Alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2532
Polymers73,2131
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-11 kcal/mol
Surface area23120 Å2
MethodPISA
2
B: Alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2532
Polymers73,2131
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-11 kcal/mol
Surface area22560 Å2
MethodPISA
3
C: Alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2532
Polymers73,2131
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-11 kcal/mol
Surface area23000 Å2
MethodPISA
4
D: Alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2532
Polymers73,2131
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-11 kcal/mol
Surface area22750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.810, 90.510, 128.550
Angle α, β, γ (deg.)105.50, 94.80, 96.15
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Alpha-glucosidase / / Glycosyl-hydrolase 97 C-terminal / oligomerisation


Mass: 73212.656 Da / Num. of mol.: 4 / Mutation: F498L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BJP75_03380, SAMN05216253_107151 / Plasmid: pCold I DNA / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A1H5YQC4, UniProt: Q8A1K0*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1257 / 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: 2.75 Å3/Da / Density % sol: 55.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 45 % (v/v) MPD, 0.2 M Lithium sulfate, 0.1 M MES-NaOH (pH 6.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: AREA DETECTOR / Date: Jul 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 125374 / % possible obs: 90 % / Redundancy: 3.2 % / CC1/2: 0.985 / Rmerge(I) obs: 0.15 / Rsym value: 0.126 / Net I/av σ(I): 6.6 / Net I/σ(I): 6.6
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 8292 / CC1/2: 0.88 / Rsym value: 0.391 / % possible all: 80.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A24

3a24


Resolution: 2.3→45.78 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.74
RfactorNum. reflection% reflection
Rfree0.2526 6265 5 %
Rwork0.2066 --
obs0.2089 125328 90.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→45.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20162 0 4 1257 21423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00520656
X-RAY DIFFRACTIONf_angle_d1.02728003
X-RAY DIFFRACTIONf_dihedral_angle_d14.3377603
X-RAY DIFFRACTIONf_chiral_restr0.042980
X-RAY DIFFRACTIONf_plane_restr0.0053645
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2975-2.32360.33411630.28113104X-RAY DIFFRACTION70
2.3236-2.35090.34532070.27973931X-RAY DIFFRACTION89
2.3509-2.37960.33142000.27563790X-RAY DIFFRACTION87
2.3796-2.40970.3181920.26143655X-RAY DIFFRACTION83
2.4097-2.44140.31371940.24673678X-RAY DIFFRACTION82
2.4414-2.47480.33452150.25454074X-RAY DIFFRACTION94
2.4748-2.51020.30352200.24584192X-RAY DIFFRACTION94
2.5102-2.54770.29672160.24834087X-RAY DIFFRACTION94
2.5477-2.58750.32632190.25644201X-RAY DIFFRACTION94
2.5875-2.62990.31252140.24844090X-RAY DIFFRACTION93
2.6299-2.67520.30682170.23854114X-RAY DIFFRACTION93
2.6752-2.72390.32140.24134068X-RAY DIFFRACTION93
2.7239-2.77620.30592170.22684138X-RAY DIFFRACTION93
2.7762-2.83290.28352140.22554077X-RAY DIFFRACTION93
2.8329-2.89450.28232130.22454048X-RAY DIFFRACTION92
2.8945-2.96180.27472100.2223986X-RAY DIFFRACTION91
2.9618-3.03590.25572090.21553975X-RAY DIFFRACTION89
3.0359-3.11790.26111940.21153671X-RAY DIFFRACTION84
3.1179-3.20970.26922010.20283825X-RAY DIFFRACTION87
3.2097-3.31320.25212220.19864223X-RAY DIFFRACTION95
3.3132-3.43160.23012180.1974137X-RAY DIFFRACTION95
3.4316-3.5690.22782180.18234139X-RAY DIFFRACTION94
3.569-3.73130.22082190.17774155X-RAY DIFFRACTION94
3.7313-3.92790.20422160.17374112X-RAY DIFFRACTION93
3.9279-4.17390.21242100.16953985X-RAY DIFFRACTION91
4.1739-4.49590.18542020.16983831X-RAY DIFFRACTION86
4.4959-4.94780.19471990.16443793X-RAY DIFFRACTION86
4.9478-5.66270.21592180.17824145X-RAY DIFFRACTION94
5.6627-7.130.22742120.20374026X-RAY DIFFRACTION92
7.13-45.78860.25742020.22023813X-RAY DIFFRACTION87

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