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- PDB-2v8m: Carbohydrate-binding of the starch binding domain of Rhizopus ory... -

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Basic information

Entry
Database: PDB / ID: 2v8m
TitleCarbohydrate-binding of the starch binding domain of Rhizopus oryzae glucoamylase in complex with beta-cyclodextrin and maltoheptaose
ComponentsGLUCOAMYLASE A
KeywordsHYDROLASE / CARBOHYDRATE BINDING
Function / homology
Function and homology information


polysaccharide metabolic process / glucan 1,4-alpha-glucosidase / glucan 1,4-alpha-glucosidase activity / metal ion binding
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 / glucan 1,4-alpha-glucosidase
Similarity search - Component
Biological speciesRHIZOPUS ORYZAE (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTung, J.-Y. / Liu, Y.-Y. / Sun, Y.-J.
CitationJournal: Biochem.J. / Year: 2008
Title: Crystal Structures of the Starch-Binding Domain from Rhizopus Oryzae Glucoamylase Reveal a Polysaccharide-Binding Path.
Authors: Tung, J.-Y. / Chang, M.D.-T. / Chou, W.-I. / Liu, Y.-Y. / Yeh, Y. / Chang, F. / Lin, S. / Qiu, Z. / Sun, Y.-J.
History
DepositionAug 9, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references / Other / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / 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_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUCOAMYLASE A
B: GLUCOAMYLASE A
C: GLUCOAMYLASE A
D: GLUCOAMYLASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,83914
Polymers46,6504
Non-polymers5,18810
Water5,693316
1
A: GLUCOAMYLASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9123
Polymers11,6631
Non-polymers1,2492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GLUCOAMYLASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0084
Polymers11,6631
Non-polymers1,3453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: GLUCOAMYLASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9123
Polymers11,6631
Non-polymers1,2492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: GLUCOAMYLASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0084
Polymers11,6631
Non-polymers1,3453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.686, 110.908, 61.161
Angle α, β, γ (deg.)90.00, 90.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
GLUCOAMYLASE A


Mass: 11662.581 Da / Num. of mol.: 4 / 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, UniProt: B7XC04*PLUS, glucan 1,4-alpha-glucosidase
#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1153.001 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,7,6/[a2122h-1a_1-5]/1-1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O
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: 2.46 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 6.5 / Details: PEG8K, AMMONIUM SULFATE, pH 6.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.9998
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 22511 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 4.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.3
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.5 / % possible all: 97.4

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.48 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1705.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1106 5.8 %RANDOM
Rwork0.238 ---
obs0.238 18953 84.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: -2.81903 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 14.8 Å2
Baniso -1Baniso -2Baniso -3
1-12.45 Å20 Å2-2.99 Å2
2---7.56 Å20 Å2
3----4.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 342 316 3966
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.4
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scbond_it1.572
X-RAY DIFFRACTIONc_scangle_it2.262.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.314 147 5.8 %
Rwork0.278 2387 -
obs--68 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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