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- PDB-8fjd: Structure of chlorophyllase from Triticum aestivum -

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Basic information

Entry
Database: PDB / ID: 8fjd
TitleStructure of chlorophyllase from Triticum aestivum
ComponentsChlorophyllase
KeywordsPLANT PROTEIN / Alpha/Beta Hydrolase
Function / homologychlorophyllase / chlorophyllase activity / : / chlorophyll catabolic process / Cutinase / PET hydrolase-like / Alpha/Beta hydrolase fold / Chlorophyllase
Function and homology information
Biological speciesTriticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.46 Å
AuthorsBoggs, D. / Jo, M. / Bridwell-Rabb, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0021240 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: A structure-function analysis of chlorophyllase reveals a mechanism for activity regulation dependent on disulfide bonds.
Authors: Jo, M. / Knapp, M. / Boggs, D.G. / Brimberry, M. / Donnan, P.H. / Bridwell-Rabb, J.
History
DepositionDec 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 15, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.type
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chlorophyllase
B: Chlorophyllase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3903
Polymers69,3502
Non-polymers401
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-19 kcal/mol
Surface area23940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.520, 197.520, 96.830
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

#1: Protein Chlorophyllase


Mass: 34674.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / Production host: Escherichia coli (E. coli) / References: UniProt: W6EIP8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.93 Å3/Da / Density % sol: 68.71 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2 M calcium acetate, 0.1 M sodium cacodylate (pH 6.5), 40% PEG300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 4.46→50 Å / Num. obs: 6846 / % possible obs: 96.8 % / Redundancy: 12.57 % / Biso Wilson estimate: 124.89 Å2 / CC1/2: 0.995 / Net I/σ(I): 7.44
Reflection shellResolution: 4.46→4.62 Å / Num. unique obs: 684 / CC1/2: 0.996

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.46→49.13 Å / SU ML: 0.4271 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.1892
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2781 342 5.02 %
Rwork0.2656 6468 -
obs0.2662 6810 95.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 129.93 Å2
Refinement stepCycle: LAST / Resolution: 4.46→49.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4481 0 1 15 4497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01234603
X-RAY DIFFRACTIONf_angle_d1.59096272
X-RAY DIFFRACTIONf_chiral_restr0.1094709
X-RAY DIFFRACTIONf_plane_restr0.01820
X-RAY DIFFRACTIONf_dihedral_angle_d10.02071670
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.46-5.620.28881680.26743207X-RAY DIFFRACTION96.73
5.62-49.130.27161740.26453261X-RAY DIFFRACTION93.47

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