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- PDB-2xqx: Structure of the family 32 carbohydrate-binding module from Strep... -

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Basic information

Entry
Database: PDB / ID: 2xqx
TitleStructure of the family 32 carbohydrate-binding module from Streptococcus pneumoniae EndoD
ComponentsENDO-BETA-N-ACETYLGLUCOSAMINIDASE D
KeywordsSUGAR BINDING PROTEIN / CARBOHYDRATE BINDING / BETA-SANDWHICH
Function / homology
Function and homology information


mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity / extracellular region / metal ion binding / cytosol
Similarity search - Function
Glycoside hydrolase, family 85 / Cytosolic endo-beta-N-acetylglucosaminidase / : / Glycosyl hydrolase family 85 / GH85 endohexosaminidases, C-terminal domain / Bacterial Ig-like domain (group 3) / Ig-like domain, bacterial type / G5 domain / G5 domain / G5 domain profile. ...Glycoside hydrolase, family 85 / Cytosolic endo-beta-N-acetylglucosaminidase / : / Glycosyl hydrolase family 85 / GH85 endohexosaminidases, C-terminal domain / Bacterial Ig-like domain (group 3) / Ig-like domain, bacterial type / G5 domain / G5 domain / G5 domain profile. / G5 / 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 / Galactose-binding domain-like / Jelly Rolls / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Putative endo-beta-N-acetylglucosaminidase / Endo-beta-N-acetylglucosaminidase D
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsAbbott, D.W. / Boraston, A.B.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structural Analysis of a Putative Family 32 Carbohydrate-Binding Module from the Streptococcus Pneumoniae Enzyme Endod.
Authors: Abbott, D.W. / Boraston, A.B.
History
DepositionSep 7, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references / Version format compliance
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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_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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDO-BETA-N-ACETYLGLUCOSAMINIDASE D
B: ENDO-BETA-N-ACETYLGLUCOSAMINIDASE D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1198
Polymers33,8022
Non-polymers3166
Water5,188288
1
A: ENDO-BETA-N-ACETYLGLUCOSAMINIDASE D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0594
Polymers16,9011
Non-polymers1583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ENDO-BETA-N-ACETYLGLUCOSAMINIDASE D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0594
Polymers16,9011
Non-polymers1583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.105, 73.510, 34.597
Angle α, β, γ (deg.)90.00, 96.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ENDO-BETA-N-ACETYLGLUCOSAMINIDASE D / ENDOD


Mass: 16901.166 Da / Num. of mol.: 2 / Fragment: CBM32, RESIDUES 804-948
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: Q93HW0, UniProt: A0A0H2UNT5*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 51.47 % / Description: NONE

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9791
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→35 Å / Num. obs: 20817 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 14.6 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 18.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 7.2 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXCDphasing
SHELXDphasing
SHELXEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.01→66.67 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.893 / SU B: 4.536 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26216 1122 5.1 %RANDOM
Rwork0.21537 ---
obs0.21782 20817 97.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.448 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å2-0.11 Å2
2--0.79 Å20 Å2
3----1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.01→66.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2279 0 18 288 2585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222345
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.9413179
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4415293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.01424.8100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42215404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0251512
X-RAY DIFFRACTIONr_chiral_restr0.0820.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211760
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_it0.6051.51460
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.10622346
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6833885
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7334.5832
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: 2.006→2.058 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 71 -
Rwork0.224 1472 -
obs--92.9 %

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