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- PDB-6l06: Crystal structure of Escherichia coli phosphatidylserine decarbox... -

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Basic information

Entry
Database: PDB / ID: 6l06
TitleCrystal structure of Escherichia coli phosphatidylserine decarboxylase (apo-form)
Components
  • Phosphatidylserine decarboxylase alpha chain
  • 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 / protein homodimerization activity / plasma membrane
Similarity search - Function
Phosphatidylserine decarboxylase / Phosphatidylserine decarboxylase, prokaryotic type 1 / Phosphatidylserine decarboxylase-related / Phosphatidylserine decarboxylase
Similarity search - Domain/homology
Phosphatidylserine decarboxylase proenzyme / Phosphatidylserine decarboxylase proenzyme
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_label_atom_id
Revision 2.1Oct 23, 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

Downloads & links

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Assembly

Deposited unit
A: Phosphatidylserine decarboxylase beta chain
E: Phosphatidylserine decarboxylase alpha chain
B: Phosphatidylserine decarboxylase beta chain
F: Phosphatidylserine decarboxylase alpha chain
C: Phosphatidylserine decarboxylase beta chain
G: Phosphatidylserine decarboxylase alpha chain
D: Phosphatidylserine decarboxylase beta chain
H: Phosphatidylserine decarboxylase alpha chain


Theoretical massNumber of molelcules
Total (without water)136,1338
Polymers136,1338
Non-polymers00
Water00
1
A: Phosphatidylserine decarboxylase beta chain
E: Phosphatidylserine decarboxylase alpha chain
B: Phosphatidylserine decarboxylase beta chain
F: 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
2
C: Phosphatidylserine decarboxylase beta chain
G: Phosphatidylserine decarboxylase alpha chain
D: Phosphatidylserine decarboxylase beta chain
H: 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)156.882, 172.012, 80.588
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Phosphatidylserine decarboxylase beta chain


Mass: 30263.859 Da / Num. of mol.: 4
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: 3769.296 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / 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
Has ligand of interestY
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: 3.99 Å3/Da / Density % sol: 69.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Tacsimate

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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: Dec 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 67495 / % possible obs: 99.5 % / Redundancy: 3.58 % / CC1/2: 0.998 / Rrim(I) all: 0.077 / Rsym value: 0.065 / Net I/σ(I): 11.35
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.03 / Num. unique obs: 20374 / CC1/2: 0.724 / Rrim(I) all: 1.009 / Rsym value: 0.858 / % possible all: 97.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→47.0599 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.39
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflection
Rfree0.2757 3431 5.08 %
Rwork0.231 --
obs0.2332 67495 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137.11 Å2 / Biso mean: 81.9066 Å2 / Biso min: 53.02 Å2
Refinement stepCycle: final / Resolution: 2.6→47.0599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9075 0 0 0 9075
Num. residues----1160
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.63550.38531220.3609227591
2.6355-2.67310.32461360.31892581100
2.6731-2.7130.32361350.30922521100
2.713-2.75540.32821220.29792529100
2.7554-2.80060.32241430.2999256299
2.8006-2.84890.33921210.32516100
2.8489-2.90070.40161500.28522537100
2.9007-2.95650.30871280.2692535100
2.9565-3.01680.34551280.28172562100
3.0168-3.08240.34491460.27532550100
3.0824-3.15410.30621480.26522515100
3.1541-3.23290.31721330.26052574100
3.2329-3.32030.32561250.25582554100
3.3203-3.4180.26071400.25052558100
3.418-3.52830.31761600.23942547100
3.5283-3.65430.29231370.24982560100
3.6543-3.80060.32231340.23572560100
3.8006-3.97350.25951420.22842573100
3.9735-4.18290.22961290.21542583100
4.1829-4.44470.20821430.20432593100
4.4447-4.78760.26011400.18942611100
4.7876-5.26880.26071240.19432601100
5.2688-6.02990.27641470.22152629100
6.0299-7.59190.24051450.23622658100
7.5919-47.05990.26831530.21722780100

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