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- PDB-7bzm: Crystal structure of rice Os3BGlu7 with glucoimidazole -

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Basic information

Entry
Database: PDB / ID: 7bzm
TitleCrystal structure of rice Os3BGlu7 with glucoimidazole
ComponentsBeta-glucosidase 7
KeywordsHYDROLASE / GH1 / rice Os3BGlu7 / beta-glucosidase / glucoimidazole
Function / homology
Function and homology information


amygdalin beta-glucosidase activity / prunasin beta-glucosidase activity / beta-L-arabinosidase activity / cellobiose glucosidase activity / beta-gentiobiose beta-glucosidase activity / beta-D-fucosidase activity / beta-mannosidase activity / glucan endo-1,3-beta-D-glucosidase activity / scopolin beta-glucosidase activity / beta-glucosidase ...amygdalin beta-glucosidase activity / prunasin beta-glucosidase activity / beta-L-arabinosidase activity / cellobiose glucosidase activity / beta-gentiobiose beta-glucosidase activity / beta-D-fucosidase activity / beta-mannosidase activity / glucan endo-1,3-beta-D-glucosidase activity / scopolin beta-glucosidase activity / beta-glucosidase / beta-galactosidase activity / beta-glucosidase activity / carbohydrate metabolic process / protein homodimerization activity / extracellular region
Similarity search - Function
Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
GLUCOIMIDAZOLE / Beta-glucosidase 7
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsPengthaisong, S. / Ketudat Cairns, J.R. / Tankrathok, A.
Funding support Thailand, 2items
OrganizationGrant numberCountry
Other governmentBRG5980015 Thailand Research Fund and Suranaree University of Technology Thailand
Other governmentFtR.15/2560 Suranaree University of Technology and Office of the Higher Education Commission under NRU Project of Thailand Thailand
CitationJournal: Biomolecules / Year: 2020
Title: Structural Basis of Specific Glucoimidazole and Mannoimidazole Binding by Os3BGlu7.
Authors: Nutho, B. / Pengthaisong, S. / Tankrathok, A. / Lee, V.S. / Ketudat Cairns, J.R. / Rungrotmongkol, T. / Hannongbua, S.
History
DepositionApr 28, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-glucosidase 7
B: Beta-glucosidase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,5079
Polymers109,4572
Non-polymers1,0507
Water8,647480
1
A: Beta-glucosidase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2865
Polymers54,7281
Non-polymers5584
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-glucosidase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2214
Polymers54,7281
Non-polymers4933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.402, 101.557, 127.458
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 1 / Auth seq-ID: 6 - 476 / Label seq-ID: 11 - 481

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999993, -0.003027, 0.002101), (-0.003028, 0.999995, -0.000275), (-0.0021, -0.000281, -0.999998)0.06917, 0.0507, 25.067591

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-glucosidase 7 / / Os3bglu7


Mass: 54728.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: BGLU7, BGLU1, Os03g0703000, LOC_Os03g49600, OSJNBa0004L11.16
Plasmid: PET32A+ / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMI(DE3) / References: UniProt: Q75I93, beta-glucosidase

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Non-polymers , 5 types, 487 molecules

#2: Chemical ChemComp-GIM / GLUCOIMIDAZOLE / (5S,6S,7R,8R)-5-(HYDROXYMETHYL)-1,5,6,7,8,8A-HEXAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL


Mass: 201.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 480 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.57 Å3/Da / Density % sol: 52.13 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 23% PEG MME 5000, 0.17 M AMMONIUM SULFATE, 0.1M MES, PH 6.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→50.01 Å / Num. obs: 47470 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.998 / Net I/σ(I): 17.3
Reflection shellResolution: 2.3→2.34 Å / Mean I/σ(I) obs: 6.6 / Num. unique obs: 2303 / CC1/2: 0.947

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RGL

2rgl


Resolution: 2.3→50.01 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.524 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.34 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.217 2314 4.9 %RANDOM
Rwork0.1766 ---
obs0.1786 44707 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.75 Å2 / Biso mean: 30.512 Å2 / Biso min: 16.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0 Å20 Å2
2--0.7 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 2.3→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7602 0 63 480 8145
Biso mean--38.72 36.41 -
Num. residues----942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197910
X-RAY DIFFRACTIONr_bond_other_d0.0020.027193
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.9310751
X-RAY DIFFRACTIONr_angle_other_deg0.942316467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1945942
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29423.616401
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.664151207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6321545
X-RAY DIFFRACTIONr_chiral_restr0.0770.21093
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219135
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022070
Refine LS restraints NCSNumber: 7344 / Type: TIGHT THERMAL / Rms dev position: 0.93 Å / Weight position: 0.5
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 180 -
Rwork0.184 3273 -
all-3453 -
obs--99.83 %

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