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- PDB-4ic6: Crystal structure of Deg8 -

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Basic information

Entry
Database: PDB / ID: 4ic6
TitleCrystal structure of Deg8
ComponentsProtease Do-like 8, chloroplastic
KeywordsHYDROLASE / Beta-barrel
Function / homology
Function and homology information


photosystem II repair / thylakoid lumen / chloroplast thylakoid / chloroplast thylakoid lumen / thylakoid / plastid / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / chloroplast / peptidase activity / serine-type endopeptidase activity / proteolysis
Similarity search - Function
PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / Pdz3 Domain / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Trypsin-like serine proteases / Thrombin, subunit H ...PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / Pdz3 Domain / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Trypsin-like serine proteases / Thrombin, subunit H / Roll / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Protease Do-like 8, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGong, W. / Sun, W. / Fan, H. / Gao, F. / Liu, L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: The structures of Arabidopsis Deg5 and Deg8 reveal new insights into HtrA proteases
Authors: Sun, W. / Gao, F. / Fan, H. / Shan, X. / Sun, R. / Liu, L. / Gong, W.
History
DepositionDec 10, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease Do-like 8, chloroplastic
B: Protease Do-like 8, chloroplastic
C: Protease Do-like 8, chloroplastic


Theoretical massNumber of molelcules
Total (without water)116,4253
Polymers116,4253
Non-polymers00
Water8,719484
1
A: Protease Do-like 8, chloroplastic
B: Protease Do-like 8, chloroplastic
C: Protease Do-like 8, chloroplastic

A: Protease Do-like 8, chloroplastic
B: Protease Do-like 8, chloroplastic
C: Protease Do-like 8, chloroplastic


Theoretical massNumber of molelcules
Total (without water)232,8496
Polymers232,8496
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area18970 Å2
ΔGint-95 kcal/mol
Surface area78400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.475, 124.175, 93.274
Angle α, β, γ (deg.)90.00, 132.41, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-675-

HOH

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Components

#1: Protein Protease Do-like 8, chloroplastic


Mass: 38808.234 Da / Num. of mol.: 3 / Fragment: UNP residues 91-448 / Mutation: S204A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DEGP8, At5g39830, K13H13.1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9LU10, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 8

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M sodium citrate tribasic dihydrate, 16.25% PEG3350, 5% jeffamine M600, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 73969 / Num. obs: 73478 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.1_743) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RFD

3rfd
PDB Unreleased entry


Resolution: 2→29.591 Å / SU ML: 0.57 / σ(F): 1.33 / Phase error: 24.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 3666 5.03 %
Rwork0.1981 --
obs0.2 72826 99.31 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.436 Å2 / ksol: 0.302 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3855 Å2-0 Å20.5149 Å2
2---5.8766 Å20 Å2
3---6.2621 Å2
Refinement stepCycle: LAST / Resolution: 2→29.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7235 0 0 484 7719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077367
X-RAY DIFFRACTIONf_angle_d1.12210045
X-RAY DIFFRACTIONf_dihedral_angle_d14.9492575
X-RAY DIFFRACTIONf_chiral_restr0.0781228
X-RAY DIFFRACTIONf_plane_restr0.0051313
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.02630.29671440.24942662100
2.0263-2.05410.26451420.23732657100
2.0541-2.08340.31251290.22852678100
2.0834-2.11450.27711570.23372667100
2.1145-2.14750.24391490.22062662100
2.1475-2.18270.29761180.24092693100
2.1827-2.22030.38741140.3069266798
2.2203-2.26070.28141310.2734258997
2.2607-2.30420.30831580.2773257497
2.3042-2.35120.23841280.21152662100
2.3512-2.40230.23621200.20222690100
2.4023-2.45810.24741450.22552677100
2.4581-2.51960.27071480.21662676100
2.5196-2.58770.2381420.21312694100
2.5877-2.66380.2821450.20912650100
2.6638-2.74970.27671470.20892665100
2.7497-2.84790.22471430.19852655100
2.8479-2.96180.26861250.21132715100
2.9618-3.09650.23561490.20662696100
3.0965-3.25950.24871370.20822642100
3.2595-3.46350.24831650.20162687100
3.4635-3.73040.21831340.2003259997
3.7304-4.10490.21411470.1682259298
4.1049-4.69690.15891580.14832686100
4.6969-5.90980.23221530.17662696100
5.9098-29.59380.22411380.189262996
Refinement TLS params.Method: refined / Origin x: 41.7058 Å / Origin y: -20.076 Å / Origin z: -51.8657 Å
111213212223313233
T0.2477 Å2-0.0847 Å20.0666 Å2-0.3095 Å20.0445 Å2--0.1595 Å2
L1.2125 °2-0.0944 °20.3511 °2-1.5365 °2-0.0185 °2--0.7854 °2
S0.0014 Å °-0.0395 Å °-0.0522 Å °0.087 Å °0.0649 Å °0.137 Å °0.1088 Å °-0.2482 Å °-0.0298 Å °
Refinement TLS groupSelection details: all

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