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- PDB-5dgr: Crystal structure of GH9 exo-beta-D-glucosaminidase PBPRA0520, gl... -

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Basic information

Entry
Database: PDB / ID: 5dgr
TitleCrystal structure of GH9 exo-beta-D-glucosaminidase PBPRA0520, glucosamine complex
ComponentsPutative endoglucanase-related protein
KeywordsHYDROLASE / Glycoside Hydrolase family 9 / alpha-alpha-6 barrel / exo-D-beta-glucosaminidase
Function / homology
Function and homology information


cellulase activity / polysaccharide catabolic process
Similarity search - Function
Cellulase, Ig-like domain / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Immunoglobulin E-set / Immunoglobulins ...Cellulase, Ig-like domain / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
2-amino-2-deoxy-beta-D-glucopyranose / Endoglucanase-related protein
Similarity search - Component
Biological speciesPhotobacterium profundum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSuzuki, K. / Honda, Y. / Fushinobu, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)22780095 Japan
Citation
Journal: Biochem.J. / Year: 2016
Title: The crystal structure of an inverting glycoside hydrolase family 9 exo-beta-D-glucosaminidase and the design of glycosynthase.
Authors: Honda, Y. / Arai, S. / Suzuki, K. / Kitaoka, M. / Fushinobu, S.
#1: Journal: Glycobiology / Year: 2011
Title: Elucidation of exo-beta-D-glucosaminidase activity of a family 9 glycoside hydrolase (PBPRA0520) from Photobacterium profundum SS9.
Authors: Honda, Y. / Shimaya, N. / Ishisaki, K. / Ebihara, M. / Taniguchi, H.
History
DepositionAug 28, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: chem_comp / citation ...chem_comp / citation / diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _chem_comp.type / _citation.journal_id_CSD ..._chem_comp.type / _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative endoglucanase-related protein
B: Putative endoglucanase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,6786
Polymers133,2732
Non-polymers4044
Water13,205733
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-42 kcal/mol
Surface area37850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.294, 102.590, 89.804
Angle α, β, γ (deg.)90.00, 97.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative endoglucanase-related protein / exo-beta-D-glucosaminidase


Mass: 66636.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photobacterium profundum (bacteria) / Gene: VV2739, PBPRA0520 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6LUT2
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Sugar ChemComp-GCS / 2-amino-2-deoxy-beta-D-glucopyranose / beta-D-glucosamine / 2-amino-2-deoxy-beta-D-glucose / 2-amino-2-deoxy-D-glucose / 2-amino-2-deoxy-glucose / D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 179.171 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO5
IdentifierTypeProgram
DGlcpNbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 733 / 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: 2.16 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10mM glucosamine, 10 % PEG 6000, 0.1M HEPES-NaOH (pH 7.5), 5% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2011
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 88029 / % possible obs: 99.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 19
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H7L

3h7l


Resolution: 1.9→28.9 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.317 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20379 4417 5 %RANDOM
Rwork0.16167 ---
obs0.16381 83494 99.2 %-
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: 24.355 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20.02 Å2
2--0.04 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.9→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9132 0 26 733 9891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0199391
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.021.92512731
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.74851139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94224.667495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.422151513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8491544
X-RAY DIFFRACTIONr_chiral_restr0.1560.21321
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0217352
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_it2.1852.2174571
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.9693.3055705
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3542.4714820
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.00319.15415746
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: 1.896→1.945 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 318 -
Rwork0.209 6013 -
obs--97.28 %

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