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- PDB-2ya0: Catalytic Module of the Multi-modular glycogen-degrading pneumoco... -

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Basic information

Entry
Database: PDB / ID: 2ya0
TitleCatalytic Module of the Multi-modular glycogen-degrading pneumococcal virulence factor SpuA
ComponentsPUTATIVE ALKALINE AMYLOPULLULANASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE
Function / homology
Function and homology information


pullulan binding / limit dextrinase activity / amylopectin binding / glycogen binding / alpha-glucan biosynthetic process / pullulanase / pullulanase activity / polysaccharide binding / calcium ion binding / cell surface / extracellular region
Similarity search - Function
Pullulanase, extracellular / SpuA, C-terminal / SpuA C-terminal / Pullulanase, carbohydrate-binding module 41 / Bacterial pullanase-associated domain / Copper resistance protein CopC/internalin, immunoglobulin-like / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Carbohydrate-binding-like fold / YSIRK type signal peptide ...Pullulanase, extracellular / SpuA, C-terminal / SpuA C-terminal / Pullulanase, carbohydrate-binding module 41 / Bacterial pullanase-associated domain / Copper resistance protein CopC/internalin, immunoglobulin-like / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Carbohydrate-binding-like fold / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Pullulanase A / Pullulanase A
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLammerts van Bueren, A. / Ficko-Blean, E. / Pluvinage, B. / Hehemann, J.H. / Higgins, M.A. / Deng, L. / Ogunniyi, A.D. / Stroeher, U.H. / Warry, N.E. / Burke, R.D. ...Lammerts van Bueren, A. / Ficko-Blean, E. / Pluvinage, B. / Hehemann, J.H. / Higgins, M.A. / Deng, L. / Ogunniyi, A.D. / Stroeher, U.H. / Warry, N.E. / Burke, R.D. / Czjzek, M. / Paton, J.C. / Vocadlo, D.J. / Boraston, A.B.
CitationJournal: Structure / Year: 2011
Title: The Conformation and Function of a Multimodular Glycogen-Degrading Pneumococcal Virulence Factor.
Authors: Lammerts Van Bueren, A. / Ficko-Blean, E. / Pluvinage, B. / Hehemann, J. / Higgins, M.A. / Deng, L. / Ogunniyi, A.D. / Stroeher, U.H. / El Warry, N. / Burke, R.D. / Czjzek, M. / Paton, J.C. ...Authors: Lammerts Van Bueren, A. / Ficko-Blean, E. / Pluvinage, B. / Hehemann, J. / Higgins, M.A. / Deng, L. / Ogunniyi, A.D. / Stroeher, U.H. / El Warry, N. / Burke, R.D. / Czjzek, M. / Paton, J.C. / Vocadlo, D.J. / Boraston, A.B.
History
DepositionFeb 17, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _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.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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE ALKALINE AMYLOPULLULANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8988
Polymers80,4441
Non-polymers4547
Water15,097838
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.574, 75.196, 87.038
Angle α, β, γ (deg.)90.00, 97.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PUTATIVE ALKALINE AMYLOPULLULANASE / PULLULANASE SPUA GH13


Mass: 80443.688 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 437-1150
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: Q97SQ7, UniProt: A0A0H2UNG0*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 838 / 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: 2.32 Å3/Da / Density % sol: 47.05 % / Description: NONE

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418
DetectorType: RIGAKU R-AXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. obs: 57697 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 3.73 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.2
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.64 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.3 / % possible all: 94.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
CrystalCleardata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FHF

2fhf


Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.406 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.22662 3085 5.1 %RANDOM
Rwork0.17177 ---
obs0.17452 57697 96.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.763 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å2-0.3 Å2
2--0.63 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5678 0 27 838 6543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0225868
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9271.9517955
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4235723
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46824.694294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45915987
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.021530
X-RAY DIFFRACTIONr_chiral_restr0.1550.2849
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214533
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_it1.1491.53566
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.84425747
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.13932302
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.754.52203
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
Rfree0.375 231 -
Rwork0.364 4053 -
obs--94.11 %

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