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- PDB-8ozs: Populus tremula stable protein 1 with N-terminal binding peptide ... -

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Basic information

Entry
Database: PDB / ID: 8ozs
TitlePopulus tremula stable protein 1 with N-terminal binding peptide extension with hemin
ComponentsStable protein 1
KeywordsPLANT PROTEIN / Hemine / Protein engineering / Biohybrid / catalysis
Function / homologypollen tube adhesion / Stress-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 / Stable protein 1
Function and homology information
Biological speciesPopulus tremula (European aspen)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSklyar, J. / Zeibaq, Y. / Bachar, O. / Yehezkeli, O. / Adir, N.
Funding support Israel, 1items
OrganizationGrant numberCountry
Other government2028751 Israel
CitationJournal: Small Science / Year: 2023
Title: A Bioengineered Stable Protein 1-Hemin Complex with Enhanced Peroxidase-Like Catalytic Properties
Authors: Sklyar, J. / Zeibaq, Y. / Bachar, O. / Yehezkeli, O. / Adir, N.
History
DepositionMay 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stable protein 1
B: Stable protein 1
C: Stable protein 1
D: Stable protein 1
E: Stable protein 1
F: Stable protein 1
G: Stable protein 1
H: Stable protein 1
I: Stable protein 1
J: Stable protein 1
K: Stable protein 1
L: Stable protein 1
M: Stable protein 1
N: Stable protein 1
O: Stable protein 1
P: Stable protein 1
Q: Stable protein 1
R: Stable protein 1
S: Stable protein 1
T: Stable protein 1
U: Stable protein 1
V: Stable protein 1
W: Stable protein 1
X: Stable protein 1


Theoretical massNumber of molelcules
Total (without water)328,35324
Polymers328,35324
Non-polymers00
Water34,7151927
1
A: Stable protein 1
B: Stable protein 1
C: Stable protein 1
D: Stable protein 1
E: Stable protein 1
F: Stable protein 1
G: Stable protein 1
H: Stable protein 1
I: Stable protein 1
J: Stable protein 1
K: Stable protein 1
L: Stable protein 1


Theoretical massNumber of molelcules
Total (without water)164,17612
Polymers164,17612
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37520 Å2
ΔGint-131 kcal/mol
Surface area46750 Å2
MethodPISA
2
M: Stable protein 1
N: Stable protein 1
O: Stable protein 1
P: Stable protein 1
Q: Stable protein 1
R: Stable protein 1
S: Stable protein 1
T: Stable protein 1
U: Stable protein 1
V: Stable protein 1
W: Stable protein 1
X: Stable protein 1


Theoretical massNumber of molelcules
Total (without water)164,17612
Polymers164,17612
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37390 Å2
ΔGint-127 kcal/mol
Surface area46830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.059, 94.372, 168.069
Angle α, β, γ (deg.)90.00, 90.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ...
Stable protein 1


Mass: 13681.366 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus tremula (European aspen) / Gene: sp1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9AR79
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1927 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 7.5% v/v Tacsimate pH 7.0, 5% v/v 2-Propanol, 0.1M Imidazole pH 7.0, 13% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 2.4→48.6 Å / Num. obs: 118649 / % possible obs: 99.8 % / Redundancy: 5.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.115 / Rrim(I) all: 0.14 / Net I/σ(I): 6.3
Reflection shellResolution: 2.4→2.44 Å / Num. unique obs: 5863 / CC1/2: 0.955

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→48.6 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2376 5992 5.07 %
Rwork0.1847 --
obs0.1874 118235 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20688 0 0 1927 22615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.847
X-RAY DIFFRACTIONf_dihedral_angle_d6.262808
X-RAY DIFFRACTIONf_chiral_restr0.0473174
X-RAY DIFFRACTIONf_plane_restr0.0073674
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.430.28742130.2293758X-RAY DIFFRACTION100
2.43-2.460.30122040.22443694X-RAY DIFFRACTION100
2.46-2.490.30211920.22163778X-RAY DIFFRACTION100
2.49-2.520.29641740.22183702X-RAY DIFFRACTION100
2.52-2.550.29732060.21233806X-RAY DIFFRACTION100
2.55-2.590.30211840.22163659X-RAY DIFFRACTION100
2.59-2.620.29052110.21863781X-RAY DIFFRACTION100
2.62-2.660.29072170.23213700X-RAY DIFFRACTION100
2.66-2.70.31022290.21613731X-RAY DIFFRACTION100
2.7-2.750.29232230.20373659X-RAY DIFFRACTION100
2.75-2.790.28042360.21083725X-RAY DIFFRACTION100
2.79-2.850.31961930.21653749X-RAY DIFFRACTION100
2.85-2.90.28771710.22123709X-RAY DIFFRACTION100
2.9-2.960.26361950.21283772X-RAY DIFFRACTION100
2.96-3.020.27051920.20753721X-RAY DIFFRACTION99
3.02-3.090.27011920.20943739X-RAY DIFFRACTION100
3.09-3.170.26291990.21383754X-RAY DIFFRACTION100
3.17-3.260.24622050.20243732X-RAY DIFFRACTION100
3.26-3.350.25772310.18393722X-RAY DIFFRACTION100
3.35-3.460.21851580.16773791X-RAY DIFFRACTION100
3.46-3.580.19352030.16153733X-RAY DIFFRACTION100
3.58-3.730.21082120.16193765X-RAY DIFFRACTION100
3.73-3.90.17121610.14263771X-RAY DIFFRACTION100
3.9-4.10.19821850.15563796X-RAY DIFFRACTION100
4.1-4.360.15592070.14173733X-RAY DIFFRACTION100
4.36-4.70.17832400.1313734X-RAY DIFFRACTION100
4.7-5.170.18521860.14323764X-RAY DIFFRACTION99
5.17-5.920.21031980.17713755X-RAY DIFFRACTION99
5.92-7.450.22622240.20013803X-RAY DIFFRACTION100
7.45-48.60.21641510.18433707X-RAY DIFFRACTION94

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