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- PDB-6ziv: Crystal structure of a Beta-glucosidase from Alicyclobacillus aci... -

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Basic information

Entry
Database: PDB / ID: 6ziv
TitleCrystal structure of a Beta-glucosidase from Alicyclobacillus acidiphilus
ComponentsBeta-glucosidase
KeywordsHYDROLASE / glucosidase
Function / homologyIODIDE ION
Function and homology information
Biological speciesAlicyclobacillus tengchongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGourlay, L.J.
CitationJournal: J.Biotechnol. / Year: 2021
Title: Producing natural vanilla extract from green vanilla beans using a beta-glucosidase from Alicyclobacillus acidiphilus.
Authors: Delgado, L. / Heckmann, C.M. / De Benedetti, S. / Nardini, M. / Gourlay, L.J. / Paradisi, F.
History
DepositionJun 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 17, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Beta-glucosidase
BBB: Beta-glucosidase
CCC: Beta-glucosidase
DDD: Beta-glucosidase
EEE: Beta-glucosidase
FFF: Beta-glucosidase
GGG: Beta-glucosidase
HHH: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)439,78632
Polymers436,7828
Non-polymers3,00424
Water35,1651952
1
AAA: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9654
Polymers54,5981
Non-polymers3673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0665
Polymers54,5981
Non-polymers4694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0535
Polymers54,5981
Non-polymers4554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
DDD: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8802
Polymers54,5981
Non-polymers2821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
EEE: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9033
Polymers54,5981
Non-polymers3052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
FFF: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9885
Polymers54,5981
Non-polymers3904
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
GGG: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0506
Polymers54,5981
Non-polymers4525
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
HHH: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8802
Polymers54,5981
Non-polymers2821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.654, 91.644, 159.342
Angle α, β, γ (deg.)91.616, 90.422, 89.988
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains A B
21Chains A C
31Chains A D
41Chains A E
51Chains A F
61Chains A G
71Chains A H
81Chains B C
91Chains B D
101Chains B E
111Chains B F
121Chains B G
131Chains B H
141Chains C D
151Chains C E
161Chains C F
171Chains C G
181Chains C H
191Chains D E
201Chains D F
211Chains D G
221Chains D H
231Chains E F
241Chains E G
251Chains E H
261Chains F G
271Chains F H
281Chains G H

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Components

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Protein , 1 types, 8 molecules AAABBBCCCDDDEEEFFFGGGHHH

#1: Protein
Beta-glucosidase /


Mass: 54597.742 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: WP_067621817 (1-449)
Source: (gene. exp.) Alicyclobacillus tengchongensis (bacteria)
Gene: SD51_06195 / Production host: Escherichia coli (E. coli) / References: beta-glucosidase

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Non-polymers , 5 types, 1976 molecules

#2: Chemical
ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / Bis-tris propane


Mass: 282.334 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1952 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.86 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: condition H3 (0.1 M Bis-Tris pH 5.5 and 25% (w/v) PEG3350) from the JCSG screen (Molecular Dimensions)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9139 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9139 Å / Relative weight: 1
ReflectionResolution: 1.55→159.2743 Å / Num. obs: 367007 / % possible obs: 91.1 % / Redundancy: 84.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.098 / Net I/σ(I): 9
Reflection shellResolution: 1.55→1.64 Å / Rmerge(I) obs: 0.561 / Num. unique obs: 18349 / CC1/2: 0.608

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
STARANISOdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: sequence

Resolution: 1.95→46.55 Å / Cor.coef. Fo:Fc: 0.85 / Cor.coef. Fo:Fc free: 0.807 / SU B: 6.593 / SU ML: 0.186 / Cross valid method: FREE R-VALUE / ESU R: 0.298 / ESU R Free: 0.225
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2963 24694 9.959 %
Rwork0.2622 223262 -
all0.266 --
obs-247956 95.977 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 11.898 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20.05 Å2-0.046 Å2
2--0.268 Å20.119 Å2
3---0.096 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28359 0 189 1952 30500
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01229687
X-RAY DIFFRACTIONr_angle_refined_deg1.311.63640408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26853554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11722.0611752
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.714154554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3415194
X-RAY DIFFRACTIONr_chiral_restr0.1040.23634
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0223662
X-RAY DIFFRACTIONr_nbd_refined0.2330.215675
X-RAY DIFFRACTIONr_nbtor_refined0.3160.219901
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2310.21925
X-RAY DIFFRACTIONr_metal_ion_refined0.3270.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3390.2111
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2250.220
X-RAY DIFFRACTIONr_mcbond_it0.8911.12714033
X-RAY DIFFRACTIONr_mcangle_it1.3871.68517519
X-RAY DIFFRACTIONr_scbond_it0.9371.1515654
X-RAY DIFFRACTIONr_scangle_it1.4141.70522846
X-RAY DIFFRACTIONr_lrange_it4.38915.04848396
X-RAY DIFFRACTIONr_ncsr_local_group_10.0860.0515182
X-RAY DIFFRACTIONr_ncsr_local_group_20.0860.0515037
X-RAY DIFFRACTIONr_ncsr_local_group_30.0910.0514988
X-RAY DIFFRACTIONr_ncsr_local_group_40.0860.0515019
X-RAY DIFFRACTIONr_ncsr_local_group_50.0860.0514971
X-RAY DIFFRACTIONr_ncsr_local_group_60.0910.0515024
X-RAY DIFFRACTIONr_ncsr_local_group_70.10.0514141
X-RAY DIFFRACTIONr_ncsr_local_group_80.0750.0515999
X-RAY DIFFRACTIONr_ncsr_local_group_90.0750.0516025
X-RAY DIFFRACTIONr_ncsr_local_group_100.0850.0515708
X-RAY DIFFRACTIONr_ncsr_local_group_110.0740.0515981
X-RAY DIFFRACTIONr_ncsr_local_group_120.0820.0515708
X-RAY DIFFRACTIONr_ncsr_local_group_130.0930.0514136
X-RAY DIFFRACTIONr_ncsr_local_group_140.0680.0515896
X-RAY DIFFRACTIONr_ncsr_local_group_150.0690.0515747
X-RAY DIFFRACTIONr_ncsr_local_group_160.0710.0515814
X-RAY DIFFRACTIONr_ncsr_local_group_170.0730.0515628
X-RAY DIFFRACTIONr_ncsr_local_group_180.0840.0514105
X-RAY DIFFRACTIONr_ncsr_local_group_190.0760.0515628
X-RAY DIFFRACTIONr_ncsr_local_group_200.0690.0515711
X-RAY DIFFRACTIONr_ncsr_local_group_210.0780.0515523
X-RAY DIFFRACTIONr_ncsr_local_group_220.0780.0514127
X-RAY DIFFRACTIONr_ncsr_local_group_230.0830.0515524
X-RAY DIFFRACTIONr_ncsr_local_group_240.0850.0515477
X-RAY DIFFRACTIONr_ncsr_local_group_250.0880.0514135
X-RAY DIFFRACTIONr_ncsr_local_group_260.080.0515571
X-RAY DIFFRACTIONr_ncsr_local_group_270.0920.0514075
X-RAY DIFFRACTIONr_ncsr_local_group_280.090.0514124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.0010.34715790.31514973X-RAY DIFFRACTION86.951
2.001-2.0550.34716950.30815454X-RAY DIFFRACTION92.0208
2.055-2.1150.33317120.30215522X-RAY DIFFRACTION95.0684
2.115-2.180.34216850.29815360X-RAY DIFFRACTION96.6489
2.18-2.2520.32715870.28914965X-RAY DIFFRACTION96.9882
2.252-2.3310.33116290.28714344X-RAY DIFFRACTION97.0708
2.331-2.4190.32614840.28513983X-RAY DIFFRACTION96.7232
2.419-2.5170.33114250.27513431X-RAY DIFFRACTION97.1234
2.517-2.6290.31315500.27412723X-RAY DIFFRACTION97.4
2.629-2.7570.32114020.2712220X-RAY DIFFRACTION97.3139
2.757-2.9070.31513210.2711686X-RAY DIFFRACTION97.3942
2.907-3.0830.28912780.26811059X-RAY DIFFRACTION97.4949
3.083-3.2960.29311620.26210399X-RAY DIFFRACTION97.1921
3.296-3.560.2810770.2489573X-RAY DIFFRACTION96.9151
3.56-3.8990.2599350.2298988X-RAY DIFFRACTION97.7635
3.899-4.3590.2289480.2078054X-RAY DIFFRACTION97.8372
4.359-5.0330.2167490.1977236X-RAY DIFFRACTION98.3011
5.033-6.1620.2436720.2166037X-RAY DIFFRACTION97.8559
6.162-8.7080.2324900.2154700X-RAY DIFFRACTION98.9703

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