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- PDB-5bza: Crystal structure of CbsA from Thermotoga neapolitana -

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Basic information

Entry
Database: PDB / ID: 5bza
TitleCrystal structure of CbsA from Thermotoga neapolitana
ComponentsBeta-N-acetylhexosaminidaseHexosaminidase
KeywordsHYDROLASE / cbsA / Thermotoga / thermostable enzyme / beta-N-acetylglucosaminidase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / Beta-N-acetylglucosaminidase CbsA
Similarity search - Component
Biological speciesThermotoga neapolitana (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.002 Å
AuthorsHa, N.C. / Kim, J.S. / Yoon, B.Y.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Crystal structure of beta-N-acetylglucosaminidase CbsA from Thermotoga neapolitana
Authors: Kim, J.S. / Yoon, B.Y. / Ahn, J. / Cha, J. / Ha, N.C.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Crystallization and preliminary X-ray crystallographic analysis of the beta-N-acetylglucosaminidase CbsA from Thermotoga neapolitana
Authors: Yoon, B.Y. / Jiao, L. / Moon, H.R. / Cha, J. / Ha, N.C.
History
DepositionJun 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-N-acetylhexosaminidase
B: Beta-N-acetylhexosaminidase
C: Beta-N-acetylhexosaminidase
D: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,25937
Polymers210,5494
Non-polymers3,71033
Water11,295627
1
A: Beta-N-acetylhexosaminidase
B: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,18619
Polymers105,2752
Non-polymers1,91117
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-139 kcal/mol
Surface area32580 Å2
MethodPISA
2
C: Beta-N-acetylhexosaminidase
D: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,07318
Polymers105,2752
Non-polymers1,79916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-118 kcal/mol
Surface area33280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.965, 158.965, 517.242
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein
Beta-N-acetylhexosaminidase / Hexosaminidase


Mass: 52637.305 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga neapolitana (bacteria) / Gene: cbsA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9AG27, beta-N-acetylhexosaminidase
#2: Chemical...
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 627 / 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: 2.99 Å3/Da / Density % sol: 58.82 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.5 1.0 M sodium acetate 0.05 M CdCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 158414 / % possible obs: 94.2 % / Redundancy: 4.5 % / Net I/σ(I): 9.25

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.002→39.741 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 31.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2763 2000 1.26 %
Rwork0.2379 --
obs0.2384 158344 93.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.002→39.741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14032 0 33 627 14692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01314339
X-RAY DIFFRACTIONf_angle_d1.48519349
X-RAY DIFFRACTIONf_dihedral_angle_d12.8345337
X-RAY DIFFRACTIONf_chiral_restr0.0632130
X-RAY DIFFRACTIONf_plane_restr0.0082509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0023-2.05240.44221200.37189369X-RAY DIFFRACTION79
2.0524-2.10790.37911340.36910458X-RAY DIFFRACTION89
2.1079-2.16990.40781370.348910747X-RAY DIFFRACTION91
2.1699-2.23990.38131400.338810911X-RAY DIFFRACTION93
2.2399-2.320.35531400.313610997X-RAY DIFFRACTION93
2.32-2.41290.29031430.285811123X-RAY DIFFRACTION94
2.4129-2.52260.29971430.277111217X-RAY DIFFRACTION95
2.5226-2.65560.34241440.263411296X-RAY DIFFRACTION95
2.6556-2.8220.28421460.247811406X-RAY DIFFRACTION96
2.822-3.03980.25831480.232511526X-RAY DIFFRACTION97
3.0398-3.34550.25491480.214211591X-RAY DIFFRACTION97
3.3455-3.82930.24211500.190611713X-RAY DIFFRACTION98
3.8293-4.82320.21881510.164311792X-RAY DIFFRACTION98
4.8232-39.74910.21311560.190212198X-RAY DIFFRACTION99

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