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- PDB-1fc9: PHOTOSYSTEM II D1 C-TERMINAL PROCESSING PROTEASE -

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Basic information

Entry
Database: PDB / ID: 1fc9
TitlePHOTOSYSTEM II D1 C-TERMINAL PROCESSING PROTEASE
ComponentsPHOTOSYSTEM II D1 PROTEASE
KeywordsHYDROLASE / D1 C-terminal processing protease / serine protease / serine-lysine catalytic dyad / PDZ domain / photosystem II / photosynthesis / x-ray crystal structure
Function / homology
Function and homology information


C-terminal processing peptidase / chloroplast thylakoid lumen / serine-type endopeptidase activity / proteolysis
Similarity search - Function
Transcription Regulator spoIIAA - #44 / C-terminal-processing peptidase S41A / tail specific protease / Tail specific protease / Peptidase family S41 / Transcription Regulator spoIIAA / PDZ domain 6 / PDZ domain / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 ...Transcription Regulator spoIIAA - #44 / C-terminal-processing peptidase S41A / tail specific protease / Tail specific protease / Peptidase family S41 / Transcription Regulator spoIIAA / PDZ domain 6 / PDZ domain / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / PDZ domain / Pdz3 Domain / ClpP/crotonase-like domain superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
C-terminal processing peptidase, chloroplastic
Similarity search - Component
Biological speciesScenedesmus obliquus (plant)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsLiao, D.I. / Qian, J. / Chisholm, D.A. / Jordan, D.B. / Diner, B.A.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Crystal structures of the photosystem II D1 C-terminal processing protease.
Authors: Liao, D.I. / Qian, J. / Chisholm, D.A. / Jordan, D.B. / Diner, B.A.
History
DepositionJul 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: PHOTOSYSTEM II D1 PROTEASE


Theoretical massNumber of molelcules
Total (without water)40,7491
Polymers40,7491
Non-polymers00
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.600, 63.100, 60.700
Angle α, β, γ (deg.)90.00, 119.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PHOTOSYSTEM II D1 PROTEASE / D1 C-TERMINAL PROCESSING PROTEASE


Mass: 40749.020 Da / Num. of mol.: 1 / Fragment: RESIDUES 77-464
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scenedesmus obliquus (plant) / Plasmid: PET-32(A)-D1P(+AM) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYS / Keywords: MATURE FORM OF THE ENZYME, NATIVE / References: UniProt: O04073
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.21 Å3/Da / Density % sol: 44.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, isopropanol, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.5 mg/mlprotein1drop
220 mMHEPES1drop
31 mMphenylboronic acid1drop
417-18 %(w/v)PEG40001reservoir
510 %(v/v)isopropanol1reservoir
60.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 3, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 113233 / Num. obs: 27619 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 18.77
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4 % / Rmerge(I) obs: 0.482 / Num. unique all: 1296 / % possible all: 95.1
Reflection
*PLUS
Num. measured all: 113233

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
TNT5Erefinement
RefinementResolution: 1.9→30 Å / σ(F): 2
Stereochemistry target values: TNT library, bond lengths 0.02, bond angles 3.0
RfactorNum. reflection
Rfree0.275 2755
Rwork0.191 -
all-27619
obs-27477
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2853 0 0 212 3065
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.6
X-RAY DIFFRACTIONt_bond_d0.015
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 2.6

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