8XUD

Crystal structure of adaptor NlpI in complex with endopeptidase MepS and PDZ-protease Prc

• PDB DOI: https://doi.org/10.2210/pdb8XUD/pdb

• Classification: PROTEIN BINDING
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-01-12 Released: 2024-06-05 
• Deposition Author(s): Tzeng, S.R., Wang, S., Huang, C.H.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.49 Å
• R-Value Free: 0.272 
• R-Value Work: 0.235 
• R-Value Observed: 0.236 

Literature

Crystal structure of lipoprotein NlpI in complex with MepS

Tzeng, S.R., Wang, S., Huang, C.H., Lin, T.S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 10-mer - A4B2C2D2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A4B2C2D1E1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 302.61 kDa 
• Atom Count: 19,377 
• Modelled Residue Count: 2,420 
• Deposited Residue Count: 2,659 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoprotein NlpI	A, B	297	Escherichia coli K-12	Mutation(s): 0  Gene Names: nlpI, yhbM, b3163, JW3132
UniProt
Find proteins for P0AFB1 (Escherichia coli (strain K12)) Explore P0AFB1  Go to UniProtKB:  P0AFB1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tail-specific protease	C, D	688	Escherichia coli K-12	Mutation(s): 2  Gene Names: prc, tsp, b1830, JW1819 EC: 3.4.21.102
UniProt
Find proteins for P23865 (Escherichia coli (strain K12)) Explore P23865  Go to UniProtKB:  P23865

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase	E [auth I], F [auth J], G [auth K], H [auth L]	168	Escherichia coli K-12	Mutation(s): 0  Gene Names: mepS, spr, yeiV, b2175, JW2163 EC: 3.4 (PDB Primary Data), 3.4.17.13 (PDB Primary Data)
UniProt
Find proteins for P0AFV4 (Escherichia coli (strain K12)) Explore P0AFV4  Go to UniProtKB:  P0AFV4

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Substrate peptide	I [auth M]	8	Escherichia coli K-12	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Substrate peptide	J [auth N]	9	Escherichia coli K-12	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	K [auth I], L [auth I], M [auth I], N [auth I], O [auth J], P [auth J], Q [auth J], R [auth K], S [auth K], T [auth K], U [auth K], V [auth K], W [auth L], X [auth L]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.49 Å
• R-Value Free: 0.272 
• R-Value Work: 0.235 
• R-Value Observed: 0.236 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 230.41	α = 90
b = 230.41	β = 90
c = 182.905	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-05 
Deposition Author(s): Tzeng, S.R., Wang, S., Huang, C.H.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-06-05
  Type: Initial release