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

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Basic information

Entry
Database: PDB / ID: 1fcf
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 / Resolution: 2.1 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: Derived calculations / Version format compliance
Revision 1.3Oct 3, 2018Group: Data collection / Derived calculations / Category: pdbx_struct_special_symmetry
Revision 1.4Oct 10, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen
Item: _entity.formula_weight / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.5Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOTOSYSTEM II D1 PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9413
Polymers40,7491
Non-polymers1922
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PHOTOSYSTEM II D1 PROTEASE
hetero molecules

A: PHOTOSYSTEM II D1 PROTEASE
hetero molecules

A: PHOTOSYSTEM II D1 PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,8239
Polymers122,2473
Non-polymers5766
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area4680 Å2
ΔGint-107 kcal/mol
Surface area49030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.753, 148.753, 100.173
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-479-

HOH

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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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)PLYS / Keywords: MATURE FORM OF THE ENZYME, NATIVE / References: UniProt: O04073
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, lithium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13.5 mg/mlprotein1drop
220 mMHEPES1drop
31 mMphenylboronic acid1drop
430-40 %(v/v)satammonium sulfate1reservoir
50.2-0.4 M1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 102 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.907
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 8, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.907 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 224983 / Num. obs: 25542 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 30.1
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5 % / Rmerge(I) obs: 0.575 / % possible all: 100
Reflection
*PLUS
% possible obs: 100 % / Num. measured all: 224983

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
TNT5Erefinement
RefinementResolution: 2.1→30 Å / σ(F): 2
Stereochemistry target values: TNT library, bond lengths 0.02 bond angles 3.0
RfactorNum. reflection
Rfree0.318 2544
Rwork0.22 -
all-25542
obs-25195
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2861 0 10 149 3020
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.7
X-RAY DIFFRACTIONt_bond_d0.015
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.22 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 2.7

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