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- PDB-6s2z: Water-soluble Chlorophyll Protein (WSCP) from Brassica oleracea v... -

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Basic information

Entry
Database: PDB / ID: 6s2z
TitleWater-soluble Chlorophyll Protein (WSCP) from Brassica oleracea var. Botrytis with Chlorophyll-b
ComponentsWater-Soluble Chlorophyll Protein
KeywordsPLANT PROTEIN / Tetramer / Plant / Brassica oleracea / Chlorophyll / Water-soluble Chlorophyll Protein / Photooxidation / Chlorophyll Carrier
Function / homology
Function and homology information


endopeptidase inhibitor activity
Similarity search - Function
Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature. / Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
CHLOROPHYLL B / Water-Soluble Chlorophyll Protein
Similarity search - Component
Biological speciesBrassica oleracea var. botrytis (cauliflower)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAgostini, A. / Meneghin, E. / Gewehr, L. / Pedron, D. / Palm, D.M. / Carbonera, D. / Paulsen, H. / Jaenicke, E. / Collini, E.
Funding support Germany, Italy, 2items
OrganizationGrant numberCountry
German Research FoundationPa 324/10-1 Germany
Italian Ministry of EducationPRIN 2015 no. 2015XBZ5YA Italy
CitationJournal: Sci Rep / Year: 2019
Title: How water-mediated hydrogen bonds affect chlorophyll a/b selectivity in Water-Soluble Chlorophyll Protein.
Authors: Agostini, A. / Meneghin, E. / Gewehr, L. / Pedron, D. / Palm, D.M. / Carbonera, D. / Paulsen, H. / Jaenicke, E. / Collini, E.
History
DepositionJun 23, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
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: Water-Soluble Chlorophyll Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0792
Polymers19,1721
Non-polymers9071
Water39622
1
A: Water-Soluble Chlorophyll Protein
hetero molecules

A: Water-Soluble Chlorophyll Protein
hetero molecules

A: Water-Soluble Chlorophyll Protein
hetero molecules

A: Water-Soluble Chlorophyll Protein
hetero molecules


  • defined by author&software
  • Evidence: homology, The structure is homologous to structure 2DRE, which is a tetramer. Due to unknown reasons structure 5HPZ, which is the same structure as our structure only differing in ...Evidence: homology, The structure is homologous to structure 2DRE, which is a tetramer. Due to unknown reasons structure 5HPZ, which is the same structure as our structure only differing in chlorphyll ligand, is annotated as dimer in the database. The tetramer with the chlorophyll ligands in the central cavity can be easily seen in the unit cell by symmetry operation from ASU.
  • 80.3 kDa, 4 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)80,3178
Polymers76,6874
Non-polymers3,6304
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area11800 Å2
ΔGint-102 kcal/mol
Surface area29640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.360, 118.330, 38.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-1103-

HOH

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Components

#1: Protein Water-Soluble Chlorophyll Protein


Mass: 19171.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brassica oleracea var. botrytis (cauliflower)
Gene: WSCP1 / Variant: Brassica oleracea var Botrytis / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q7GDB3
#2: Chemical ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 47.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 10% PEG 3350, 0.1 M Ammonium dihydrogen phosphate, pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 10, 2018 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→19.72 Å / Num. obs: 7149 / % possible obs: 99.5 % / Redundancy: 7.51 % / CC1/2: 0.995 / Rmerge(I) obs: 0.18 / Net I/σ(I): 15.82
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 7.51 % / Mean I/σ(I) obs: 3.78 / Num. unique obs: 526 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSVERSION Mar 15, 2019data reduction
XSCALEVERSION Mar 15, 2019data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HPZ

5hpz


Resolution: 2.5→19.72 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.854 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.615 / ESU R Free: 0.329 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2836 358 5 %RANDOM
Rwork0.2175 ---
obs0.2207 6790 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 90.28 Å2 / Biso mean: 24.86 Å2 / Biso min: 7.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.5→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1323 0 66 22 1411
Biso mean--17.52 19.44 -
Num. residues----175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121432
X-RAY DIFFRACTIONr_angle_refined_deg2.3461.7191971
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3135174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43523.77453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41515212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.886154
X-RAY DIFFRACTIONr_chiral_restr0.0930.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021083
LS refinement shellResolution: 2.5→2.564 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 26 -
Rwork0.315 492 -
all-518 -
obs--99.62 %

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