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- PDB-5il9: Crystal structure of Deg9 -

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Basic information

Entry
Database: PDB / ID: 5il9
TitleCrystal structure of Deg9
ComponentsProtease Do-like 9
KeywordsHYDROLASE / Deg Protease / Octamer
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / serine-type endopeptidase activity / nucleolus / proteolysis / nucleus
Similarity search - Function
N-terminal domain of MutM-like DNA repair proteins - #20 / Protease Do-like, PDZ domain / Protease Do-like, PDZ domain superfamily / PDZ domain / N-terminal domain of MutM-like DNA repair proteins / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / PDZ superfamily ...N-terminal domain of MutM-like DNA repair proteins - #20 / Protease Do-like, PDZ domain / Protease Do-like, PDZ domain superfamily / PDZ domain / N-terminal domain of MutM-like DNA repair proteins / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / PDZ superfamily / Alpha-Beta Barrel / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Alpha Beta
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsOuyang, M. / Liu, L. / Li, X.Y. / Zhao, S. / Zhang, L.X.
CitationJournal: Nat Plants / Year: 2017
Title: The crystal structure of Deg9 reveals a novel octameric-type HtrA protease
Authors: Ouyang, M. / Li, X. / Zhao, S. / Pu, H. / Shen, J. / Adam, Z. / Clausen, T. / Zhang, L.
History
DepositionMar 4, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease Do-like 9
B: Protease Do-like 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,9494
Polymers124,7652
Non-polymers1842
Water11,818656
1
A: Protease Do-like 9
B: Protease Do-like 9
hetero molecules

A: Protease Do-like 9
B: Protease Do-like 9
hetero molecules

A: Protease Do-like 9
B: Protease Do-like 9
hetero molecules

A: Protease Do-like 9
B: Protease Do-like 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)499,79616
Polymers499,0598
Non-polymers7378
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area28610 Å2
ΔGint-75 kcal/mol
Surface area142450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.047, 132.047, 154.157
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Protease Do-like 9


Mass: 62382.383 Da / Num. of mol.: 2 / Fragment: UNP residues 65-592
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DEGP9, At5g40200, MSN9.10, MSN9.100 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9FL12, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 656 / 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: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium acetate, 0.1M Hepes pH7.5, 45% v/v MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 66736 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 25.2
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.787

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FLN

4fln


Resolution: 2.2→39.932 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2278 2992 5.02 %
Rwork0.1804 56614 -
obs0.1828 59606 89.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.24 Å2 / Biso mean: 34.4454 Å2 / Biso min: 12.6 Å2
Refinement stepCycle: final / Resolution: 2.2→39.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6994 0 12 656 7662
Biso mean--56.56 37.14 -
Num. residues----920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087160
X-RAY DIFFRACTIONf_angle_d0.9379732
X-RAY DIFFRACTIONf_chiral_restr0.0631132
X-RAY DIFFRACTIONf_plane_restr0.0061250
X-RAY DIFFRACTIONf_dihedral_angle_d15.232568
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2003-2.23630.2584620.19171234129641
2.2363-2.27490.2279690.19821443151248
2.2749-2.31630.249940.21321680177456
2.3163-2.36080.2337970.21681941203864
2.3608-2.4090.30091080.21462266237476
2.409-2.46140.2781650.21512783294893
2.4614-2.51860.28931610.21542988314999
2.5186-2.58160.26551440.213430183162100
2.5816-2.65140.2691510.209130203171100
2.6514-2.72940.28311680.208329733141100
2.7294-2.81750.25231570.200630693226100
2.8175-2.91810.27331500.194129833133100
2.9181-3.03490.23291480.188530383186100
3.0349-3.1730.23951860.18130053191100
3.173-3.34020.19161600.173930023162100
3.3402-3.54940.2131530.168730403193100
3.5494-3.82320.21461830.161830083191100
3.8232-4.20760.19691580.153330223180100
4.2076-4.81550.2031440.144830403184100
4.8155-6.06360.21691560.180130493205100
6.0636-39.93860.20471780.18763012319098

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