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- PDB-3qo6: Crystal structure analysis of the plant protease Deg1 -

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Basic information

Entry
Database: PDB / ID: 3qo6
TitleCrystal structure analysis of the plant protease Deg1
Components
  • (peptide) x 4
  • Protease Do-like 1, chloroplastic
KeywordsPHOTOSYNTHESIS / protease / HtrA / pH-sensor / hydrolase
Function / homology
Function and homology information


photosystem II repair / thylakoid lumen / chloroplast thylakoid / thylakoid / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / chloroplast thylakoid membrane / serine-type peptidase activity / chloroplast / protein catabolic process / serine-type endopeptidase activity ...photosystem II repair / thylakoid lumen / chloroplast thylakoid / thylakoid / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / chloroplast thylakoid membrane / serine-type peptidase activity / chloroplast / protein catabolic process / serine-type endopeptidase activity / identical protein binding / nucleus / cytosol
Similarity search - Function
PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / Pdz3 Domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Trypsin-like serine proteases ...PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / Pdz3 Domain / PDZ domain profile. / 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 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsClausen, T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Structural adaptation of the plant protease Deg1 to repair photosystem II during light exposure.
Authors: Kley, J. / Schmidt, B. / Boyanov, B. / Stolt-Bergner, P.C. / Kirk, R. / Ehrmann, M. / Knopf, R.R. / Naveh, L. / Adam, Z. / Clausen, T.
History
DepositionFeb 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 5, 2012Group: Derived calculations
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 999AUTHOR STATES THAT THE PEPTIDES WERE CO-PURIFIED AND CO-CRYSTALLIZED WITH THE DEG1 PROTEIN FROM E. ...AUTHOR STATES THAT THE PEPTIDES WERE CO-PURIFIED AND CO-CRYSTALLIZED WITH THE DEG1 PROTEIN FROM E.COLI, HOWEVER THEIR PRECISE ORIGIN IS UNKNOWN. THEY ARE MODELED AS ALA IN THE DEPOSITED PDB FILE AND HAVE BEEN CHANGED TO UNK DURING PROCESSING.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease Do-like 1, chloroplastic
B: Protease Do-like 1, chloroplastic
C: Protease Do-like 1, chloroplastic
D: peptide
E: peptide
F: peptide
G: peptide
H: peptide
I: peptide


Theoretical massNumber of molelcules
Total (without water)112,7629
Polymers112,7629
Non-polymers00
Water2,486138
1
A: Protease Do-like 1, chloroplastic
B: Protease Do-like 1, chloroplastic
C: Protease Do-like 1, chloroplastic
D: peptide
E: peptide
F: peptide
G: peptide
H: peptide
I: peptide

A: Protease Do-like 1, chloroplastic
B: Protease Do-like 1, chloroplastic
C: Protease Do-like 1, chloroplastic
D: peptide
E: peptide
F: peptide
G: peptide
H: peptide
I: peptide


Theoretical massNumber of molelcules
Total (without water)225,52518
Polymers225,52518
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area19990 Å2
ΔGint-98 kcal/mol
Surface area78930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.135, 126.135, 328.303
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

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Protein/peptide , 4 types, 6 molecules DEHIFG

#2: Protein/peptide peptide


Mass: 613.749 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide peptide


Mass: 358.434 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli)
#4: Protein/peptide peptide


Mass: 443.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli)
#5: Protein/peptide peptide


Mass: 273.330 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli)

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Protein / Non-polymers , 2 types, 141 molecules ABC

#1: Protein Protease Do-like 1, chloroplastic


Mass: 36785.508 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g27925, Deg1, DEGP, DEGP1, K16N12.18 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O22609, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 3.52 Å3/Da / Density % sol: 65.07 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 5.2
Details: sodium citrate, ammonium sulfate, lithium sulfate, pH 5.2, vapor diffusion, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2010
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 57809 / Num. obs: 53034 / % possible obs: 98.1 % / Observed criterion σ(F): -1000 / Observed criterion σ(I): -1000 / Rmerge(I) obs: 0.054 / Χ2: 1.083 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.590.92652011.045198.4
2.59-2.690.74952701.128199.7
2.69-2.810.50253161.061100
2.81-2.960.32953031.0061100
2.96-3.150.1853540.9711100
3.15-3.390.09953490.987199.9
3.39-3.730.05953571.031199.6
3.73-4.260.03953531.023198.7
4.26-5.350.0353101.172196.4
5.35-200.03252211.42189.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MH7

3mh7


Resolution: 2.5→15 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2678 2636 4.9 %RANDOM
Rwork0.2154 ---
all0.228 54001 --
obs0.228 52796 97.8 %-
Solvent computationBsol: 75.6883 Å2
Displacement parametersBiso max: 154.97 Å2 / Biso mean: 85.1888 Å2 / Biso min: 34.27 Å2
Baniso -1Baniso -2Baniso -3
1-7.854 Å20 Å20 Å2
2--7.854 Å20 Å2
3----15.707 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7428 0 0 138 7566
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_d1.71
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3peptideAS.par

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