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- PDB-5ilb: Crystal structure of protease domain of Deg2 linked with the PDZ ... -

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Basic information

Entry
Database: PDB / ID: 5ilb
TitleCrystal structure of protease domain of Deg2 linked with the PDZ domain of Deg9
ComponentsProtease Do-like 2, chloroplastic,Protease Do-like 9
KeywordsHYDROLASE / Deg2 / Deg9 / fusion protein
Function / homology
Function and homology information


photosystem II repair / chloroplast stromal thylakoid / chloroplast organization / chloroplast envelope / chloroplast stroma / chloroplast thylakoid membrane / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / chloroplast / protein catabolic process ...photosystem II repair / chloroplast stromal thylakoid / chloroplast organization / chloroplast envelope / chloroplast stroma / chloroplast thylakoid membrane / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / chloroplast / protein catabolic process / serine-type endopeptidase activity / nucleolus / proteolysis / nucleus / cytosol
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 / Trypsin / Alpha-Beta Barrel / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Alpha Beta
Similarity search - Domain/homology
Protease Do-like 2, chloroplastic / Protease Do-like 9
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.852 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 2, chloroplastic,Protease Do-like 9
B: Protease Do-like 2, chloroplastic,Protease Do-like 9


Theoretical massNumber of molelcules
Total (without water)105,2492
Polymers105,2492
Non-polymers00
Water18,8261045
1
A: Protease Do-like 2, chloroplastic,Protease Do-like 9
B: Protease Do-like 2, chloroplastic,Protease Do-like 9

A: Protease Do-like 2, chloroplastic,Protease Do-like 9
B: Protease Do-like 2, chloroplastic,Protease Do-like 9

A: Protease Do-like 2, chloroplastic,Protease Do-like 9
B: Protease Do-like 2, chloroplastic,Protease Do-like 9


Theoretical massNumber of molelcules
Total (without water)315,7476
Polymers315,7476
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area27400 Å2
ΔGint-54 kcal/mol
Surface area106290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.093, 106.093, 255.956
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-724-

HOH

21A-1040-

HOH

31A-1083-

HOH

41A-1109-

HOH

51B-694-

HOH

61B-1044-

HOH

71B-1046-

HOH

81B-1082-

HOH

91B-1113-

HOH

101B-1114-

HOH

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Components

#1: Protein Protease Do-like 2, chloroplastic,Protease Do-like 9


Mass: 52624.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fusion protein of protease domain of Deg2 (residues 110-315 of O82261, DEGP2_ARATH) and the PDZ domain of Deg9 (residues 326-592 of Q9FL12 DEGP9_ARATH).
Source: (gene. exp.) Arabidopsis thaliana (thale cress)
Gene: DEGP2, At2g47940, F17A22.33, T9J23.7, DEGP9, At5g40200, MSN9.10, MSN9.100
Production host: Escherichia coli (E. coli)
References: UniProt: O82261, UniProt: Q9FL12, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1045 / 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: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1M Magnesium formate, 0.2 M Sodium thiocyanate, 15% w/v PEG 3350

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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: Nov 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 91028 / % possible obs: 99.8 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 16.9
Reflection shellLowest resolution: 1.92 Å / Redundancy: 1.85 % / Rmerge(I) obs: 0.734

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IL9

5il9


Resolution: 1.852→26.523 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.8
RfactorNum. reflection% reflection
Rfree0.2248 4395 5.01 %
Rwork0.1895 --
obs0.1912 87664 95.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 67.41 Å2 / Biso mean: 22.52 Å2 / Biso min: 1.1 Å2
Refinement stepCycle: final / Resolution: 1.852→26.523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7165 0 0 1045 8210
Biso mean---32.25 -
Num. residues----929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047375
X-RAY DIFFRACTIONf_angle_d0.92210031
X-RAY DIFFRACTIONf_chiral_restr0.071157
X-RAY DIFFRACTIONf_plane_restr0.0041294
X-RAY DIFFRACTIONf_dihedral_angle_d13.0722721
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8523-1.87340.3133850.25431445153050
1.8734-1.89540.2954950.2531837193264
1.8954-1.91850.311140.25952365247982
1.9185-1.94280.29051510.24792697284893
1.9428-1.96840.24631500.22612857300799
1.9684-1.99530.25011540.229428653019100
1.9953-2.02380.25271370.206728943031100
2.0238-2.0540.25411560.213428853041100
2.054-2.08610.25861500.203228773027100
2.0861-2.12030.24121370.211929043041100
2.1203-2.15680.20951470.198529273074100
2.1568-2.1960.22471740.196528723046100
2.196-2.23820.231430.202729153058100
2.2382-2.28390.24861440.198328823026100
2.2839-2.33350.22781630.199528933056100
2.3335-2.38780.26841480.20228813029100
2.3878-2.44750.24221360.209229213057100
2.4475-2.51360.23371600.208228813041100
2.5136-2.58750.26791390.211229083047100
2.5875-2.67090.26991910.21328213012100
2.6709-2.76630.26941690.211428943063100
2.7663-2.87690.23471620.20328783040100
2.8769-3.00770.22441390.193928873026100
3.0077-3.1660.20011430.190429083051100
3.166-3.3640.21421550.188728613016100
3.364-3.62320.24421360.169129333069100
3.6232-3.98670.19691550.165328773032100
3.9867-4.5610.1661580.145728753033100
4.561-5.73680.17281410.153329103051100
5.7368-26.5260.20211630.16722719288294
Refinement TLS params.Method: refined / Origin x: 28.4541 Å / Origin y: -37.6679 Å / Origin z: 36.7825 Å
111213212223313233
T-0.0902 Å2-0.0875 Å20.0262 Å2-0.0232 Å2-0.0453 Å2--0.0571 Å2
L0.3404 °2-0.1598 °20.2017 °2-0.2158 °2-0.0214 °2--0.8661 °2
S-0.0188 Å °-0.0303 Å °-0.0174 Å °0.0127 Å °0.031 Å °0.1294 Å °0.0943 Å °-0.3767 Å °0.0308 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA112 - 577
2X-RAY DIFFRACTION1allB114 - 576
3X-RAY DIFFRACTION1allS1 - 1049

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