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- PDB-4bfo: Crystal Structure of the Starch-Binding Domain from Rhizopus oryz... -

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Basic information

Entry
Database: PDB / ID: 4bfo
TitleCrystal Structure of the Starch-Binding Domain from Rhizopus oryzae Glucoamylase in Complex with isomaltotriose
ComponentsGLUCOAMYLASEGlucan 1,4-a-glucosidase
KeywordsHYDROLASE / CARBOHYDRATE BINDING
Function / homology
Function and homology information


polysaccharide metabolic process / glucan 1,4-alpha-glucosidase / glucan 1,4-alpha-glucosidase activity
Similarity search - Function
Carbohydrate binding type-21 domain / CBM21 (carbohydrate binding type-21) domain / CBM21 domain superfamily / Carbohydrate/starch-binding module (family 21) / CBM21 (carbohydrate binding type-21) domain profile. / Glucoamylase / : / Glucoamylase active site region signature. / GH15-like domain / Glycosyl hydrolases family 15 ...Carbohydrate binding type-21 domain / CBM21 (carbohydrate binding type-21) domain / CBM21 domain superfamily / Carbohydrate/starch-binding module (family 21) / CBM21 (carbohydrate binding type-21) domain profile. / Glucoamylase / : / Glucoamylase active site region signature. / GH15-like domain / Glycosyl hydrolases family 15 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
glucan 1,4-alpha-glucosidase
Similarity search - Component
Biological speciesRHIZOPUS ORYZAE (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.175 Å
AuthorsChu, C.H. / Li, K.M. / Lin, S.W. / Sun, Y.J.
CitationJournal: Proteins / Year: 2014
Title: Crystal Structures of Starch Binding Domain from Rhizopus Oryzae Glucoamylase in Complex with Isomaltooligosaccharide: Insights Into Polysaccharide Binding Mechanism of Cbm21 Family.
Authors: Chu, C. / Li, K. / Lin, S. / Chang, M.D. / Jiang, T. / Sun, Y.
History
DepositionMar 21, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 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: GLUCOAMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1672
Polymers11,6631
Non-polymers5041
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.529, 25.866, 61.085
Angle α, β, γ (deg.)90.00, 124.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein GLUCOAMYLASE / Glucan 1,4-a-glucosidase


Mass: 11662.581 Da / Num. of mol.: 1 / Fragment: STARCH BINDING DOMAIN, RESIDUES 26-131
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHIZOPUS ORYZAE (fungus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2VC81, glucan 1,4-alpha-glucosidase
#2: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a6-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsALPHA-D-GLUCOSE (GLC): EACH ALPHA-D-GLUCOSE MOLECULE IS CONNECTED BY ALPHA-1,6 GLYCOSIDIC LINKAGES
Sequence detailsILE 53 IS A CLONING VARIANT FROM A LOCAL STRAIN OF R. ORYZAE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growDetails: 0.1 M NA-CITRATE PH 5.6, 18% PEG4000, 0.2 M NH4-ACETATE

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.9762
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.17→50 Å / Num. obs: 36109 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 6.64 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 30.25
Reflection shellResolution: 1.17→1.21 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 6.44 / % possible all: 86.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V8L

2v8l


Resolution: 1.175→25.318 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 14.24 / Stereochemistry target values: ML
Details: ASN101 LIES BEYOND THE REASONABLE RANGE OF RAMACHANDRAN PLOT DUE TO ITS INTERACTION WITH THE SURROUNDING RESIDUES. THUS, ASN101 IS LIMITED IN A RIGID CONDITION.
RfactorNum. reflection% reflection
Rfree0.1693 1809 5 %
Rwork0.1564 --
obs0.1571 36101 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.88 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 10.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.0998 Å20 Å2-1.4265 Å2
2---0.5234 Å20 Å2
3---0.4236 Å2
Refinement stepCycle: LAST / Resolution: 1.175→25.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms826 0 34 219 1079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005883
X-RAY DIFFRACTIONf_angle_d1.1891204
X-RAY DIFFRACTIONf_dihedral_angle_d32.94343
X-RAY DIFFRACTIONf_chiral_restr0.082135
X-RAY DIFFRACTIONf_plane_restr0.005147
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1754-1.21740.17241580.15663389X-RAY DIFFRACTION99
1.2174-1.26610.15521630.15063427X-RAY DIFFRACTION100
1.2661-1.32370.17561960.14653441X-RAY DIFFRACTION100
1.3237-1.39350.16021590.14683445X-RAY DIFFRACTION100
1.3935-1.48080.16341920.143422X-RAY DIFFRACTION100
1.4808-1.59510.14171770.13523444X-RAY DIFFRACTION100
1.5951-1.75560.17691800.14533466X-RAY DIFFRACTION100
1.7556-2.00960.14721950.15323404X-RAY DIFFRACTION98
2.0096-2.53150.1922030.15843301X-RAY DIFFRACTION96
2.5315-25.32380.16411860.16323553X-RAY DIFFRACTION98

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