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- PDB-7cnz: Crystal structure of 10PE bound PSD from E. coli (2.70 A) -

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Basic information

Entry
Database: PDB / ID: 7cnz
TitleCrystal structure of 10PE bound PSD from E. coli (2.70 A)
Components
  • Phosphatidylserine decarboxylase alpha chain
  • Phosphatidylserine decarboxylase beta chain
KeywordsLYASE / Phosphatidylserine decarboxylase / pyruvoyl-dependent decarboxylase / auto-cleaved / serine protease / product bound / 8:0/8:0 PE / 8:0/8:0 Phosphatidylethanolamine / 8:0 PE / Schiff base reduction by NaCNBH3 / Conjugation / MEMBRANE PROTEIN
Function / homology
Function and homology information


phosphatidylserine decarboxylase / phosphatidylserine decarboxylase activity / phosphatidylethanolamine biosynthetic process / plasma membrane
Similarity search - Function
Phosphatidylserine decarboxylase / Phosphatidylserine decarboxylase, prokaryotic type 1 / Phosphatidylserine decarboxylase-related / Phosphatidylserine decarboxylase
Similarity search - Domain/homology
1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / PHOSPHATE ION / Phosphatidylserine decarboxylase proenzyme
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 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 / 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 2.1Nov 6, 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: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,88415
Polymers132,5098
Non-polymers2,3757
Water18010
1
A: Phosphatidylserine decarboxylase beta chain
B: Phosphatidylserine decarboxylase alpha chain
C: Phosphatidylserine decarboxylase beta chain
D: Phosphatidylserine decarboxylase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4908
Polymers66,2544
Non-polymers1,2354
Water362
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3957
Polymers66,2544
Non-polymers1,1403
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.723, 102.373, 168.993
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
11LEULEULEULEUAA13 - 25213 - 252
21LEULEULEULEUCC13 - 25213 - 252
12LEULEULEULEUAA9 - 2529 - 252
22LEULEULEULEUEE9 - 2529 - 252
13LEULEULEULEUAA9 - 2529 - 252
23LEULEULEULEUGG9 - 2529 - 252
14THRTHRSERSERBB255 - 2862 - 33
24THRTHRSERSERDD255 - 2862 - 33
15THRTHRHISHISBB255 - 2922 - 39
25THRTHRHISHISFF255 - 2922 - 39
16THRTHRHISHISBB255 - 2912 - 38
26THRTHRHISHISHH255 - 2912 - 38
17LEULEULEULEUCC13 - 25213 - 252
27LEULEULEULEUEE13 - 25213 - 252
18LEULEULEULEUCC13 - 25213 - 252
28LEULEULEULEUGG13 - 25213 - 252
19THRTHRSERSERDD255 - 2862 - 33
29THRTHRSERSERFF255 - 2862 - 33
110THRTHRSERSERDD255 - 2862 - 33
210THRTHRSERSERHH255 - 2862 - 33
111LEULEUGLYGLYEE7 - 2537 - 253
211LEULEUGLYGLYGG7 - 2537 - 253
112THRTHRHISHISFF255 - 2912 - 38
212THRTHRHISHISHH255 - 2912 - 38

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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-PEX / 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 522.632 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H49NO8P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.58 Å3/Da / Density % sol: 52.33 % / Description: Rhombus
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M Tris pH 8.5, 25% w/v PEG 3350

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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: 0.97957 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 2.7→29.47 Å / Num. obs: 38760 / % possible obs: 99.9 % / Redundancy: 13.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.052 / Rrim(I) all: 0.192 / Net I/σ(I): 12.6 / Num. measured all: 529506
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
2.7-2.8213.12.6496122146660.5310.7572.7571100
9.35-29.4712.40.0291261010150.9990.0090.0363.196.8

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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: 2.7→29.43 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.911 / SU B: 19.757 / SU ML: 0.367 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.301 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2763 1981 5.1 %RANDOM
Rwork0.227 ---
obs0.2295 36717 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 172.77 Å2 / Biso mean: 66.398 Å2 / Biso min: 37.31 Å2
Baniso -1Baniso -2Baniso -3
1-7.14 Å2-0 Å20 Å2
2---3.77 Å2-0 Å2
3----3.37 Å2
Refinement stepCycle: final / Resolution: 2.7→29.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8655 0 15 10 8680
Biso mean--98.39 52.06 -
Num. residues----1131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0138867
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178182
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.65712097
X-RAY DIFFRACTIONr_angle_other_deg1.1911.59318845
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.04751118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95922.045396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.484151317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2441548
X-RAY DIFFRACTIONr_chiral_restr0.0570.21180
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029916
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021844
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A72840.08
12C72840.08
21A74980.07
22E74980.07
31A71790.09
32G71790.09
41B6320.12
42D6320.12
51B7480.08
52F7480.08
61B7110.17
62H7110.17
71C72900.08
72E72900.08
81C71740.08
82G71740.08
91D6300.11
92F6300.11
101D6400.09
102H6400.09
111E72150.09
112G72150.09
121F7030.17
122H7030.17
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 148 -
Rwork0.375 2673 -
all-2821 -
obs--100 %

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