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- PDB-5a55: The native structure of GH101 from Streptococcus pneumoniae TIGR4 -

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Basic information

Entry
Database: PDB / ID: 5a55
TitleThe native structure of GH101 from Streptococcus pneumoniae TIGR4
ComponentsENDO-ALPHA-N-ACETYLGALACTOSAMINIDASE
KeywordsHYDROLASE / ENDO-BETA-N-ACETYLGALACTOSAMINIDASE / GLYCOSIDE HYDROLASE FAMILY 101 / GH101 / T-ANTIGEN / MUCIN DEGRADATION
Function / homology
Function and homology information


endo-alpha-N-acetylgalactosaminidase / endo-alpha-N-acetylgalactosaminidase activity / carbohydrate binding / extracellular region / metal ion binding
Similarity search - Function
: / Endo-alpha-N-acetylgalactosaminidase, domain 5 / Glycosyl hydrolase 101, beta-sandwich domain / Galactose-binding domain-like / Endo-alpha-N-acetylgalactosaminidase, N-terminal / Galactose mutarotase-like fold domain / Endo-alpha-N-acetylgalactosaminidase / Glycosyl hydrolase 101 beta sandwich domain / Galactose-binding domain-like / Endo-alpha-N-acetylgalactosaminidase N-terminal domain ...: / Endo-alpha-N-acetylgalactosaminidase, domain 5 / Glycosyl hydrolase 101, beta-sandwich domain / Galactose-binding domain-like / Endo-alpha-N-acetylgalactosaminidase, N-terminal / Galactose mutarotase-like fold domain / Endo-alpha-N-acetylgalactosaminidase / Glycosyl hydrolase 101 beta sandwich domain / Galactose-binding domain-like / Endo-alpha-N-acetylgalactosaminidase N-terminal domain / Galactose mutarotase-like fold domain / Endo-alpha-N-acetylgalactosaminidase / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / YSIRK type signal peptide / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / YSIRK Gram-positive signal peptide / Beta-galactosidase; Chain A, domain 5 / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Galactose-binding domain-like / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Galactose-binding-like domain superfamily / Distorted Sandwich / Glycosidases / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Endo-alpha-N-acetylgalactosaminidase
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGregg, K.J. / Suits, M.D.L. / Deng, L. / Vocadlo, D.J. / Boraston, A.B.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Analysis of a Family 101 Glycoside Hydrolase in Complex with Carbohydrates Reveals Insights Into its Mechanism.
Authors: Gregg, K.J. / Suits, M.D.L. / Deng, L. / Vocadlo, D.J. / Boraston, A.B.
History
DepositionJun 16, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Oct 28, 2015Group: Database references
Revision 1.3Oct 9, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status / reflns
Item: _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs
Revision 1.4May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)125,2938
Polymers124,9531
Non-polymers3397
Water29,6711647
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.260, 89.130, 88.570
Angle α, β, γ (deg.)90.00, 110.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ENDO-ALPHA-N-ACETYLGALACTOSAMINIDASE


Mass: 124953.156 Da / Num. of mol.: 1 / Fragment: RESIDUES 317-1425
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2MGH6, endo-alpha-N-acetylgalactosaminidase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1647 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.34 % / Description: NONE
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 1:1 ratio of protein to 25% (w/v) polyethylene glycol (PEG) 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946
DetectorType: MARRESAEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 88792 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 47.1
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.6 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 1.85→89.09 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.567 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17879 4686 5 %RANDOM
Rwork0.14253 ---
obs0.14439 88792 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.429 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.88 Å2
2--0.04 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.85→89.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8716 0 13 1647 10376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0198982
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.91912178
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77651114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.90725458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65151490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2771537
X-RAY DIFFRACTIONr_chiral_restr0.1120.21284
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026958
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7431.0654414
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2281.5935518
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3181.1844568
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 358 -
Rwork0.181 6454 -
obs--97.97 %

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