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- PDB-7cnx: Crystal structure of Apo PSD from E. coli (2.63 A) -

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Basic information

Entry
Database: PDB / ID: 7cnx
TitleCrystal structure of Apo PSD from E. coli (2.63 A)
Components
  • Phosphatidylserine decarboxylase alpha chain
  • Phosphatidylserine decarboxylase beta chain
KeywordsLYASE / Phosphatidylserine decarboxylase / pyruvoyl-dependent decarboxylase / auto-cleaved / serine protease / Apo state / MEMBRANE PROTEIN
Function / homologyphosphatidylserine decarboxylase / Phosphatidylserine decarboxylase / Phosphatidylserine decarboxylase, prokaryotic type 1 / Phosphatidylserine decarboxylase-related / Phosphatidylserine decarboxylase / phosphatidylserine decarboxylase activity / phosphatidylethanolamine biosynthetic process / plasma membrane / Phosphatidylserine decarboxylase proenzyme
Function and homology information
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.63 Å
AuthorsKim, J. / Cho, G.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Sci Rep / Year: 2021
Title: Structural insights into phosphatidylethanolamine formation in bacterial membrane biogenesis.
Authors: Cho, G. / Lee, E. / Kim, J.
History
DepositionAug 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
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 / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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
B: Phosphatidylserine decarboxylase alpha chain
C: Phosphatidylserine decarboxylase beta chain
D: Phosphatidylserine decarboxylase alpha chain
E: Phosphatidylserine decarboxylase beta chain
F: Phosphatidylserine decarboxylase alpha chain
G: Phosphatidylserine decarboxylase beta chain
H: Phosphatidylserine decarboxylase alpha chain


Theoretical massNumber of molelcules
Total (without water)132,5098
Polymers132,5098
Non-polymers00
Water25214
1
A: Phosphatidylserine decarboxylase beta chain
B: Phosphatidylserine decarboxylase alpha chain
C: Phosphatidylserine decarboxylase beta chain
D: Phosphatidylserine decarboxylase alpha chain


Theoretical massNumber of molelcules
Total (without water)66,2544
Polymers66,2544
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Phosphatidylserine decarboxylase beta chain
F: Phosphatidylserine decarboxylase alpha chain
G: Phosphatidylserine decarboxylase beta chain
H: Phosphatidylserine decarboxylase alpha chain


Theoretical massNumber of molelcules
Total (without water)66,2544
Polymers66,2544
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.896, 101.847, 170.095
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23G
14B
24D
15B
25F
16B
26H
17C
27E
18C
28G
19D
29F
110D
210H
111E
211G
112F
212H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLEULEUAA14 - 25214 - 252
21PROPROLEULEUCC14 - 25214 - 252
12SERSERLEULEUAA8 - 2528 - 252
22SERSERLEULEUEE8 - 2528 - 252
13GLNGLNLEULEUAA10 - 25210 - 252
23GLNGLNLEULEUGG10 - 25210 - 252
14THRTHRSERSERBB255 - 2862 - 33
24THRTHRSERSERDD255 - 2862 - 33
15THRTHRHISHISBB255 - 2902 - 37
25THRTHRHISHISFF255 - 2902 - 37
16THRTHRHISHISBB255 - 2912 - 38
26THRTHRHISHISHH255 - 2912 - 38
17PROPROLEULEUCC14 - 25214 - 252
27PROPROLEULEUEE14 - 25214 - 252
18PROPROLEULEUCC14 - 25214 - 252
28PROPROLEULEUGG14 - 25214 - 252
19THRTHRSERSERDD255 - 2862 - 33
29THRTHRSERSERFF255 - 2862 - 33
110THRTHRSERSERDD255 - 2862 - 33
210THRTHRSERSERHH255 - 2862 - 33
111GLNGLNLEULEUEE10 - 25210 - 252
211GLNGLNLEULEUGG10 - 25210 - 252
112THRTHRHISHISFF255 - 2902 - 37
212THRTHRHISHISHH255 - 2902 - 37

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

#1: Protein
Phosphatidylserine decarboxylase beta chain


Mass: 28645.170 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: psd, FAZ83_09855 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A6D2XQZ0, phosphatidylserine decarboxylase
#2: Protein/peptide
Phosphatidylserine decarboxylase alpha chain


Mass: 4482.063 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: psd, FAZ83_09855 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A6D2XQZ0, phosphatidylserine decarboxylase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
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: 2.61 Å3/Da / Density % sol: 52.9 % / Description: Rhombus
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.18 M Ammonium acetate, 0.09 M Tris pH 8.5, 22.5% w/v PEG 3350, 5% v/v Jeffamine M-600 pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: LN2 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.63→48.83 Å / Num. obs: 42052 / % possible obs: 100 % / Redundancy: 8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.055 / Rrim(I) all: 0.156 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.63-2.738.22.6093550343280.4410.9642.7831100
9.84-48.786.20.0355268950.9990.0130.03250.798.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
MxDCdata collection
XDSdata reduction
Aimless0.7.4data scaling
MOLREPphasing
Coot0.8.9.2model building
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.63→48.78 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.899 / SU B: 18.561 / SU ML: 0.359 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.726 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2884 2056 4.9 %RANDOM
Rwork0.231 ---
obs0.2338 39931 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 166.96 Å2 / Biso mean: 62.835 Å2 / Biso min: 35.48 Å2
Baniso -1Baniso -2Baniso -3
1-3.68 Å20 Å20 Å2
2--0.12 Å2-0 Å2
3----3.8 Å2
Refinement stepCycle: final / Resolution: 2.63→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8431 0 0 14 8445
Biso mean---51.36 -
Num. residues----1130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0138644
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177802
X-RAY DIFFRACTIONr_angle_refined_deg1.431.64211813
X-RAY DIFFRACTIONr_angle_other_deg1.2331.56817906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.94151120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69421.658398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.375151230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9171550
X-RAY DIFFRACTIONr_chiral_restr0.060.21166
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029876
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021858
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A70580.08
12C70580.08
21A72550.07
22E72550.07
31A70330.07
32G70330.07
41B6000.12
42D6000.12
51B7180.07
52F7180.07
61B6690.13
62H6690.13
71C70860.08
72E70860.08
81C69690.07
82G69690.07
91D6050.11
92F6050.11
101D6220.1
102H6220.1
111E69800.08
112G69800.08
121F6610.13
122H6610.13
LS refinement shellResolution: 2.63→2.698 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 145 -
Rwork0.359 2908 -
all-3053 -
obs--100 %

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