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- PDB-6l07: Crystal structure of Escherichia coli phosphatidylserine decarbox... -

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Basic information

Entry
Database: PDB / ID: 6l07
TitleCrystal structure of Escherichia coli phosphatidylserine decarboxylase (PE-bound form)
Components
  • (Phosphatidylserine decarboxylase alpha chain) x 2
  • Phosphatidylserine decarboxylase beta chain
KeywordsLYASE / Phosphatidylserine / Phosphatidylethanolamine / Membrane
Function / homology
Function and homology information


phosphatidylserine decarboxylase / phosphatidylserine decarboxylase activity / phosphatidylethanolamine biosynthetic process / zymogen activation / protein autoprocessing / plasma membrane
Similarity search - Function
Phosphatidylserine decarboxylase-related / Phosphatidylserine decarboxylase / Phosphatidylserine decarboxylase, prokaryotic type 1 / Phosphatidylserine decarboxylase
Similarity search - Domain/homology
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Phosphatidylserine decarboxylase proenzyme / Phosphatidylserine decarboxylase proenzyme
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsWatanabe, Y. / Watanabe, S.
CitationJournal: Structure / Year: 2020
Title: Structural Basis for Phosphatidylethanolamine Biosynthesis by Bacterial Phosphatidylserine Decarboxylase.
Authors: Watanabe, Y. / Watanabe, Y. / Watanabe, S.
History
DepositionSep 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 22, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 2.0Oct 6, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.ptnr1_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphatidylserine decarboxylase beta chain
I: Phosphatidylserine decarboxylase alpha chain
B: Phosphatidylserine decarboxylase beta chain
J: Phosphatidylserine decarboxylase alpha chain
C: Phosphatidylserine decarboxylase beta chain
K: Phosphatidylserine decarboxylase alpha chain
D: Phosphatidylserine decarboxylase beta chain
N: Phosphatidylserine decarboxylase alpha chain
E: Phosphatidylserine decarboxylase beta chain
L: Phosphatidylserine decarboxylase alpha chain
F: Phosphatidylserine decarboxylase beta chain
O: Phosphatidylserine decarboxylase alpha chain
G: Phosphatidylserine decarboxylase beta chain
M: Phosphatidylserine decarboxylase alpha chain
H: Phosphatidylserine decarboxylase beta chain
P: Phosphatidylserine decarboxylase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,91521
Polymers272,19516
Non-polymers3,7205
Water0
1
A: Phosphatidylserine decarboxylase beta chain
I: Phosphatidylserine decarboxylase alpha chain
E: Phosphatidylserine decarboxylase beta chain
L: Phosphatidylserine decarboxylase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5266
Polymers68,0384
Non-polymers1,4882
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphatidylserine decarboxylase beta chain
J: Phosphatidylserine decarboxylase alpha chain
D: Phosphatidylserine decarboxylase beta chain
N: Phosphatidylserine decarboxylase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7965
Polymers68,0524
Non-polymers7441
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Phosphatidylserine decarboxylase beta chain
K: Phosphatidylserine decarboxylase alpha chain
G: Phosphatidylserine decarboxylase beta chain
M: Phosphatidylserine decarboxylase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5266
Polymers68,0384
Non-polymers1,4882
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: Phosphatidylserine decarboxylase beta chain
O: Phosphatidylserine decarboxylase alpha chain
H: Phosphatidylserine decarboxylase beta chain
P: Phosphatidylserine decarboxylase alpha chain


Theoretical massNumber of molelcules
Total (without water)68,0664
Polymers68,0664
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)218.191, 218.191, 143.798
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
Phosphatidylserine decarboxylase beta chain


Mass: 30263.859 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3) / Variant: C43 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C43
References: UniProt: A0A446DLT6, UniProt: P0A8K1*PLUS, phosphatidylserine decarboxylase
#2: Protein/peptide
Phosphatidylserine decarboxylase alpha chain


Mass: 3755.313 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3) / Variant: C43 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C43
References: UniProt: A0A446DLT6, UniProt: P0A8K1*PLUS, phosphatidylserine decarboxylase
#3: Protein/peptide Phosphatidylserine decarboxylase alpha chain


Mass: 3769.296 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3) / Variant: C43 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C43
References: UniProt: A0A446DLT6, UniProt: P0A8K1*PLUS, phosphatidylserine decarboxylase
#4: Chemical
ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE / Discrete optimized protein energy


Mass: 744.034 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
Has ligand of interestY

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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: 3.63 Å3/Da / Density % sol: 66.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: pentaerythritol ethoxylate, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 45175 / % possible obs: 99.8 % / Redundancy: 5.38 % / CC1/2: 0.999 / Rrim(I) all: 0.084 / Rsym value: 0.076 / Net I/σ(I): 12.3
Reflection shellResolution: 3.6→3.82 Å / Redundancy: 5.19 % / Mean I/σ(I) obs: 1.47 / Num. unique obs: 14239 / CC1/2: 0.598 / Rrim(I) all: 1.136 / Rsym value: 1.021 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→49.2441 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.7
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflection
Rfree0.2891 2327 5.15 %
Rwork0.241 --
obs0.2434 45175 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 235.33 Å2 / Biso mean: 154.5922 Å2 / Biso min: 91.77 Å2
Refinement stepCycle: final / Resolution: 3.6→49.2441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18179 0 0 0 18179
Num. residues----2319
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.6-3.67250.38631370.352249599
3.6725-3.75230.36391200.34412520100
3.7523-3.83960.35451470.3152506100
3.8396-3.93560.32731310.30352493100
3.9356-4.04190.33611310.30022532100
4.0419-4.16080.2991310.30292508100
4.1608-4.2950.29771660.27662496100
4.295-4.44850.32441330.27472524100
4.4485-4.62640.31091350.26282496100
4.6264-4.83680.32011220.25182550100
4.8368-5.09160.27341380.2452499100
5.0916-5.41020.27161430.23862517100
5.4102-5.82730.31671430.25462532100
5.8273-6.41260.31741330.26352530100
6.4126-7.33790.28471410.25372522100
7.3379-9.2350.24161330.18682552100
9.235-49.24410.26221430.1965257699

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