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- PDB-1fc6: PHOTOSYSTEM II D1 C-TERMINAL PROCESSING PROTEASE -

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Basic information

Entry
Database: PDB / ID: 1fc6
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 / SYNCHROTRON / MAD, treating MAD data as a special case of MIR / Resolution: 1.8 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 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)41,0201
Polymers41,0201
Non-polymers00
Water6,341352
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.300, 64.450, 63.730
Angle α, β, γ (deg.)90.00, 122.11, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-778-

HOH

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Components

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


Mass: 41019.566 Da / Num. of mol.: 1 / Fragment: RESIDUES 77-464 / Mutation: L132M, L210M
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(MET-) / References: UniProt: O04073
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.36 Å3/Da / Density % sol: 47.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: PEG 4000, isopropanol, HEPES, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 7.5
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: 102 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.9946
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 20, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9946 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 258532 / Num. obs: 35489 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.28 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 18
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.394 / Num. unique all: 1737 / % possible all: 99
Reflection
*PLUS
Num. measured all: 258532

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Processing

Software
NameVersionClassification
PHASESphasing
TNT5Erefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD, treating MAD data as a special case of MIR
Resolution: 1.8→30 Å / σ(F): 2
Stereochemistry target values: TNT library, Bond lengths 0.02 bond angles 3.00
RfactorNum. reflection% reflection
Rfree0.237 3520 -
Rwork0.168 --
all-35489 -
obs-35171 99.1 %
Solvent computationSolvent model: Method implemented in the refinement program TNT
Bsol: 248.14 Å2 / ksol: 0.86085 e/Å3
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2853 0 0 352 3205
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.4
X-RAY DIFFRACTIONt_bond_d0.018
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 2.4

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