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- PDB-2x05: Inhibition of the exo-beta-D-glucosaminidase CsxA by a glucosamin... -

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Basic information

Entry
Database: PDB / ID: 2x05
TitleInhibition of the exo-beta-D-glucosaminidase CsxA by a glucosamine- configured castanospermine and an amino-australine analogue
ComponentsEXO-BETA-D-GLUCOSAMINIDASE
KeywordsHYDROLASE / EXO-BETA-D-GLUCOSAMINIDASE / GLYCOSIDE HYDROLASE / GH2 / CSXA / GLYCOSIDASE
Function / homology
Function and homology information


exo-1,4-beta-D-glucosaminidase / exo-1,4-beta-D-glucosaminidase activity / chitin catabolic process / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / extracellular region
Similarity search - Function
Exo-beta-D-glucosaminidase, Ig-fold domain / Exo-beta-D-glucosaminidase/Endo-beta-mannosidase / Exo-beta-D-glucosaminidase Ig-fold domain / Glycosyl hydrolase 2 galactose-binding domain-like / Carbohydrate binding module (family 35) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 ...Exo-beta-D-glucosaminidase, Ig-fold domain / Exo-beta-D-glucosaminidase/Endo-beta-mannosidase / Exo-beta-D-glucosaminidase Ig-fold domain / Glycosyl hydrolase 2 galactose-binding domain-like / Carbohydrate binding module (family 35) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / AMINO-CASTANOSPERMINE / Exo-beta-D-glucosaminidase
Similarity search - Component
Biological speciesAMYCOLATOPSIS ORIENTALIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPluvinage, B. / Ghinet, M.G. / Brzezinski, R. / Boraston, A.B. / Stubbs, K.A.
CitationJournal: Org.Biomol.Chem. / Year: 2009
Title: Inhibition of the Exo-Beta-D-Glucosaminidase Csxa by a Glucosamine-Configured Castanospermine and an Amino-Australine Analogue.
Authors: Pluvinage, B. / Ghinet, M.G. / Brzezinski, R. / Boraston, A.B. / Stubbs, K.A.
History
DepositionDec 5, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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_asym_id / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.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_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: EXO-BETA-D-GLUCOSAMINIDASE
B: EXO-BETA-D-GLUCOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,78023
Polymers221,2682
Non-polymers2,51221
Water21,7081205
1
A: EXO-BETA-D-GLUCOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,83411
Polymers110,6341
Non-polymers1,20010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: EXO-BETA-D-GLUCOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,94612
Polymers110,6341
Non-polymers1,31211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.120, 121.800, 91.560
Angle α, β, γ (deg.)90.00, 90.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein EXO-BETA-D-GLUCOSAMINIDASE


Mass: 110633.797 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-1032
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AMYCOLATOPSIS ORIENTALIS (bacteria) / Plasmid: PFD666 / Production host: STREPTOMYCES LIVIDANS (bacteria) / Strain (production host): TK24 / References: UniProt: Q56F26, exo-1,4-beta-D-glucosaminidase
#2: Chemical ChemComp-X05 / AMINO-CASTANOSPERMINE / (1S,6S,7R,8R,8AR)-6-AMINOOCTAHYDROINDOLIZINE-1,7,8-TRIOL


Mass: 188.224 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16N2O3
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1205 / 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: 2.1 Å3/Da / Density % sol: 43.32 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-3 / Wavelength: 0.97946
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 83030 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 4.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
CCP4SCALEdata scaling
MERGEINTENSITIESdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VZS

2vzs


Resolution: 2.3→43.79 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.882 / SU B: 7.232 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.351 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.24816 4151 5 %RANDOM
Rwork0.18401 ---
obs0.18723 78855 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.848 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20.3 Å2
2--0.28 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13034 0 45 1205 14284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02213408
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.9418307
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.51451708
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3524.301579
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.314152054
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0291570
X-RAY DIFFRACTIONr_chiral_restr0.0910.22019
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110334
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_it0.511.58473
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.943213641
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.51634935
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3464.54663
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 313 -
Rwork0.235 5823 -
obs--99.84 %

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