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- PDB-8s4e: Dimeric Alpha-beta barrel protein from Brassica rapa subsp.pekinensis -

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Basic information

Entry
Database: PDB / ID: 8s4e
TitleDimeric Alpha-beta barrel protein from Brassica rapa subsp.pekinensis
ComponentsGenome assembly, chromosome: A10
KeywordsHYDROLASE / Dimeric Alpha-beta Barrel Protein
Function / homologyStress-response A/B barrel domain-containing protein HS1/DABB1-like / Stress responsive alpha-beta barrel / Stress responsive A/B Barrel Domain / Stress-response A/B barrel domain profile. / Stress responsive A/B Barrel Domain / Dimeric alpha-beta barrel / Stress-response A/B barrel domain-containing protein
Function and homology information
Biological speciesBrassica rapa (field mustard)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsPick, L.M. / Tang, Q. / Ansorge-Schumacher, M. / Grogan, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/T01430X/1 United Kingdom
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: SilE-R and SilE-S-DABB Proteins Catalying Enantiospecific Hydrolysis of Organosilyl Ethers.
Authors: Pick, L.M. / Oehme, V. / Hartmann, J. / Wenzlaff, J. / Tang, Q. / Grogan, G. / Ansorge-Schumacher, M.B.
History
DepositionFeb 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome assembly, chromosome: A10
B: Genome assembly, chromosome: A10


Theoretical massNumber of molelcules
Total (without water)27,6672
Polymers27,6672
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-17 kcal/mol
Surface area12060 Å2
Unit cell
Length a, b, c (Å)92.370, 92.370, 70.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Genome assembly, chromosome: A10


Mass: 13833.698 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brassica rapa (field mustard) / Gene: BRAA10T43907Z, BRAPAZ1V2_A10P19140.2, BRARA_J01461 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A397XUN4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.15 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 500 mM Bis-tris propane pH 6.5; 40% (w/v) PEG 3350; 500 mM NaI

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.98→53.1 Å / Num. obs: 24712 / % possible obs: 100 % / Redundancy: 20.4 % / CC1/2: 1 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.15 / Net I/σ(I): 13.8
Reflection shellResolution: 1.98→2.03 Å / Rmerge(I) obs: 1.58 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1696 / CC1/2: 0.83 / Rpim(I) all: 0.97

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→53.1 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.038 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20683 1273 5.2 %RANDOM
Rwork0.17046 ---
obs0.17237 23415 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.685 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20.59 Å20 Å2
2--1.18 Å2-0 Å2
3----3.83 Å2
Refinement stepCycle: 1 / Resolution: 1.98→53.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1747 0 0 125 1872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121791
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161641
X-RAY DIFFRACTIONr_angle_refined_deg1.8191.8032428
X-RAY DIFFRACTIONr_angle_other_deg0.6491.7393782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5245223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.1852
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53110279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1080.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022050
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02400
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2673.822898
X-RAY DIFFRACTIONr_mcbond_other3.2653.822898
X-RAY DIFFRACTIONr_mcangle_it4.416.8241119
X-RAY DIFFRACTIONr_mcangle_other4.4116.8291120
X-RAY DIFFRACTIONr_scbond_it5.0764.317893
X-RAY DIFFRACTIONr_scbond_other5.074.309892
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.5947.6861310
X-RAY DIFFRACTIONr_long_range_B_refined8.4838.572022
X-RAY DIFFRACTIONr_long_range_B_other8.41437.791993
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 95 -
Rwork0.28 1716 -
obs--100 %

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