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- PDB-2vq4: Carbohydrate-binding of the starch binding domain of Rhizopus ory... -

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Basic information

Entry
Database: PDB / ID: 2vq4
TitleCarbohydrate-binding of the starch binding domain of Rhizopus oryzae glucoamylase in complex with beta-cyclodextrin and maltoheptaose
ComponentsGLUCOAMYLASE A
KeywordsHYDROLASE / RHIZOPUS ORYZAE GLUCOAMYLASE / CARBOHYDRATE BINDING / STARCH BINDING DOMAIN
Function / homology
Function and homology information


glucan 1,4-alpha-glucosidase / glucan 1,4-alpha-glucosidase activity / fungal-type vacuole / polysaccharide catabolic process
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: 1.25 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. / Chou, W. / Liu, Y.-Y. / Yeh, Y. / Chang, F. / Lin, S. / Qiu, Z. / Sun, Y.-J.
History
DepositionMar 11, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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

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Assembly

Deposited unit
A: GLUCOAMYLASE A


Theoretical massNumber of molelcules
Total (without water)11,6631
Polymers11,6631
Non-polymers00
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)26.635, 33.894, 93.389
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GLUCOAMYLASE A


Mass: 11662.581 Da / Num. of mol.: 1 / Fragment: STARCH BINDING DOMAIN, RESIDUES 26-131 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ILE 53 IS A CLONING VARIANT FROM A LOCAL STRAIN OF R. ORYZAE
Source: (gene. exp.) RHIZOPUS ORYZAE (fungus) / Plasmid: PET23A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q2VC81, glucan 1,4-alpha-glucosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 78 TO ILE
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: 1.81 Å3/Da / Density % sol: 0.32 % / Description: NONE
Crystal growDetails: 25% PEG4000

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.9732
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9732 Å / Relative weight: 1
ReflectionResolution: 1.25→30 Å / Num. obs: 23978 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 11.6 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 31.5
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 6.7 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V8L

2v8l


Resolution: 1.25→30 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.288 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.053 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 6, 42, 99, AND 101 ARE DISORDERED ALTERNATE POSITIONS ARE PRESENT FOR SIDE CHAIN OF RESIDUES SER 8, GLN10, SER 19, THR37, SER 44, ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 6, 42, 99, AND 101 ARE DISORDERED ALTERNATE POSITIONS ARE PRESENT FOR SIDE CHAIN OF RESIDUES SER 8, GLN10, SER 19, THR37, SER 44, SER57, GLU68, AND SER89. HENCE THEIR ALTERNATE INDICATORS ARE A AND B. THEY CONCERNED HAVE OCCUPANCY BETWEEN 0.0 AND 1.0 AND WERE REFINED AS DESCRIBED ABOVE. OCCUPANCY VALUES LOWER THAN 1. 0 APPEARED TO JUSTIFY BETTER THE ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.169 1219 5.1 %RANDOM
Rwork0.146 ---
obs0.147 22701 98.5 %-
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: 12.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2--0.4 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms818 0 0 210 1028
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022865
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.911176
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9365105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.13125.71442
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.28515135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1070.2125
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02668
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.2410
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.2626
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2173
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2421.5535
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8632856
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5823392
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.064.5320
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: 1.25→1.28 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.173 74
Rwork0.159 1567

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