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- PDB-4bbw: The crystal structure of Sialidase VPI 5482 (BTSA) from Bacteroid... -

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Basic information

Entry
Database: PDB / ID: 4bbw
TitleThe crystal structure of Sialidase VPI 5482 (BTSA) from Bacteroides thetaiotaomicron
ComponentsSIALIDASE (NEURAMINIDASE)
KeywordsHYDROLASE / NEURAMIDASE
Function / homology
Function and homology information


ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase activity / : / intracellular membrane-bounded organelle / membrane / cytoplasm
Similarity search - Function
Sialidase, N-terminal / N-terminal domain of BNR-repeat neuraminidase / Immunoglobulin-like - #1290 / Trypanosome sialidase / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller ...Sialidase, N-terminal / N-terminal domain of BNR-repeat neuraminidase / Immunoglobulin-like - #1290 / Trypanosome sialidase / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Sialidase (Neuraminidase)
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsPark, K.-H. / Song, H.-N. / Jung, T.-Y. / Lee, M.-H. / Woo, E.-J.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Structural and Biochemical Characterization of the Broad Substrate Specificity of Bacteroides Thetaiotaomicron Commensal Sialidase.
Authors: Park, K. / Kim, M. / Ahn, H. / Lee, D. / Kim, J. / Kim, Y. / Woo, E.
History
DepositionSep 28, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SIALIDASE (NEURAMINIDASE)


Theoretical massNumber of molelcules
Total (without water)61,7631
Polymers61,7631
Non-polymers00
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)141.377, 94.023, 50.533
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein SIALIDASE (NEURAMINIDASE) / SIALIDASE VPI5482


Mass: 61763.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8AAK9, exo-alpha-sialidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.78 Å3/Da / Density % sol: 55.37 % / Description: NONE
Crystal growpH: 4.2
Details: 1.6M NAH2PO4,0.4M K2HPO4, PHOSPHATE-CITRATE 100MM PH4.2

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.31→50 Å / Num. obs: 52341 / % possible obs: 91.1 % / Observed criterion σ(I): 1 / Redundancy: 3.48 % / Rmerge(I) obs: 0.28 / Net I/σ(I): 12.5
Reflection shellResolution: 2.31→2.43 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.72 / % possible all: 68.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.3→44.61 Å / SU ML: 0.33 / σ(F): 1.34 / Phase error: 29.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2592 1454 5.1 %
Rwork0.2084 --
obs0.2109 28688 93.37 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.123 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 46.123 Å2
Baniso -1Baniso -2Baniso -3
1--22.0326 Å20 Å20 Å2
2---10.0386 Å20 Å2
3---32.0711 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4080 0 0 238 4318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094170
X-RAY DIFFRACTIONf_angle_d1.3165652
X-RAY DIFFRACTIONf_dihedral_angle_d15.4291541
X-RAY DIFFRACTIONf_chiral_restr0.095628
X-RAY DIFFRACTIONf_plane_restr0.005725
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.38220.32021250.30212148X-RAY DIFFRACTION76
2.3822-2.47760.35621280.27452311X-RAY DIFFRACTION81
2.4776-2.59040.28761320.26832474X-RAY DIFFRACTION86
2.5904-2.72690.31811450.25452649X-RAY DIFFRACTION92
2.7269-2.89770.39821430.24732868X-RAY DIFFRACTION99
2.8977-3.12140.28091380.23072903X-RAY DIFFRACTION99
3.1214-3.43540.26791700.21622869X-RAY DIFFRACTION99
3.4354-3.93230.2231730.19162924X-RAY DIFFRACTION100
3.9323-4.95320.23991350.16252974X-RAY DIFFRACTION100
4.9532-44.61820.20441650.18613114X-RAY DIFFRACTION100

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