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- PDB-2zxq: Crystal structure of endo-alpha-N-acetylgalactosaminidase from Bi... -

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Basic information

Entry
Database: PDB / ID: 2zxq
TitleCrystal structure of endo-alpha-N-acetylgalactosaminidase from Bifidobacterium longum (EngBF)
ComponentsEndo-alpha-N-acetylgalactosaminidase
KeywordsHYDROLASE / Broken TIM barrel / Glycosidase
Function / homology
Function and homology information


endo-alpha-N-acetylgalactosaminidase / mucinaminylserine mucinaminidase activity / glycopeptide alpha-N-acetylgalactosaminidase activity / metabolic process / carbohydrate binding / integral component of membrane / metal ion binding
Endo-alpha-N-acetylgalactosaminidase / Concanavalin A-like lectin/glucanase domain superfamily / Endo-alpha-N-acetylgalactosaminidase, N-terminal / Galactose-binding domain-like / Glycosyl hydrolase 101, beta-sandwich domain / Endo-alpha-N-acetylgalactosaminidase / Glycoside hydrolase-type carbohydrate-binding / Glycosyl hydrolase, all-beta / Galactose-binding-like domain superfamily / F5/8 type C domain ...Endo-alpha-N-acetylgalactosaminidase / Concanavalin A-like lectin/glucanase domain superfamily / Endo-alpha-N-acetylgalactosaminidase, N-terminal / Galactose-binding domain-like / Glycosyl hydrolase 101, beta-sandwich domain / Endo-alpha-N-acetylgalactosaminidase / Glycoside hydrolase-type carbohydrate-binding / Glycosyl hydrolase, all-beta / Galactose-binding-like domain superfamily / F5/8 type C domain / Carboxypeptidase-like, regulatory domain superfamily / Coagulation factor 5/8 C-terminal domain / Glycosyl hydrolase 101 beta sandwich domain / Galactose-binding domain-like / Endo-alpha-N-acetylgalactosaminidase N-terminal / Galactose mutarotase-like fold domain / Coagulation factors 5/8 type C domain (FA58C) profile. / Galactose mutarotase-like fold domain
Endo-alpha-N-acetylgalactosaminidase
Biological speciesBifidobacterium longum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsSuzuki, R. / Katayama, T. / Ashida, H. / Yamamoto, K. / Kitaoka, M. / Fushinobu, S.
Citation
Journal: J.Biochem. / Year: 2009
Title: Crystallographic and mutational analyses of substrate recognition of endo-{alpha}-N-acetylgalactosaminidase from Bifidobacterium longum.
Authors: Suzuki, R. / Katayama, T. / Kitaoka, M. / Kumagai, H. / Wakagi, T. / Shoun, H. / Ashida, H. / Yamamoto, K. / Fushinobu, S.
#1: Journal: J.Biol.Chem. / Year: 2005
Title: Identification and molecular cloning of a novel glycoside hydrolase family of core 1 type O-glycan-specific endo-alpha-N-acetylgalactosaminidase from Bifidobacterium longum.
Authors: Fujita, K. / Oura, F. / Nagamine, N. / Katayama, T. / Hiratake, J. / Sakata, K. / Kumagai, H. / Yamamoto, K.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJan 5, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endo-alpha-N-acetylgalactosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,3698
Polymers149,7951
Non-polymers5747
Water25,2751403
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)192.267, 192.267, 123.017
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein/peptide Endo-alpha-N-acetylgalactosaminidase


Mass: 149794.797 Da / Num. of mol.: 1 / Fragment: residues 340-1694
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum (bacteria) / Strain: JCM1217 / Gene: engBF / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus(DE3)-RIL
References: UniProt: Q3T552, endo-alpha-N-acetylgalactosaminidase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Manganese
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / 2-Methyl-2,4-pentanediol
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1403 / Source method: isolated from a natural source / Formula: H2O / Water
Sequence detailsTHE GLY1123SER MUTATION IS AN UNINTENDED MUTATION DUE TO PCR-ERROR INTRODUCED DURING THE CLONING PROCESS.

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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: 4.38 Å3/Da / Density % sol: 71.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 0.1M MES-NaOH, 3% PEG 20000, 25% MPD, 0.2M NaCl, 0.01M MnCl2, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.96787, 0.97923, 0.97939, 0.96416
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 17, 2008
RadiationMonochromator: triangular silicon (111) crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.967871
20.979231
30.979391
40.964161
ReflectionResolution: 2→50 Å / Num. all: 174089 / Num. obs: 172447 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 27.4 Å2 / Rsym value: 0.075 / Net I/σ(I): 27.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 17314 / Rsym value: 0.467 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→36.49 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.353 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19564 8598 5 %RANDOM
Rwork0.17203 ---
Obs0.17324 163203 98.71 %-
All-172447 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.743 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20 Å2
2--0.03 Å20 Å2
3----0.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.101 Å0.103 Å
Refinement stepCycle: LAST / Resolution: 2→36.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9070 0 4 1427 10501
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0140.0229271
r_bond_other_d
r_angle_refined_deg1.4081.93112571
r_angle_other_deg
r_dihedral_angle_1_deg6.65551176
r_dihedral_angle_2_deg37.21625.518444
r_dihedral_angle_3_deg13.409151518
r_dihedral_angle_4_deg16.3751534
r_chiral_restr0.1010.21363
r_gen_planes_refined0.0060.027122
r_gen_planes_other
r_nbd_refined0.1960.24485
r_nbd_other
r_nbtor_refined0.3040.26341
r_nbtor_other
r_xyhbond_nbd_refined0.1320.21263
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined0.1790.244
r_symmetry_vdw_other
r_symmetry_hbond_refined0.1340.242
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it0.8421.55950
r_mcbond_other
r_mcangle_it1.36229274
r_scbond_it2.1433881
r_scangle_it3.2854.53297
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 637 -
Rwork0.21 12104 -
Obs--99.32 %

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