8XUP

Crystal structure of lipoprotein NlpI in complex with MepS

• PDB DOI: https://doi.org/10.2210/pdb8XUP/pdb

• Classification: PROTEIN BINDING
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-01-13 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: 2.80 Å
• R-Value Free: 0.221 
• R-Value Work: 0.171 
• R-Value Observed: 0.173 

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 6-mer - A4B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A4B2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 289.52 kDa 
• Atom Count: 18,080 
• Modelled Residue Count: 2,189 
• Deposited Residue Count: 2,532 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoprotein NlpI	A, B, C, D	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
Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase	E, F, G, H, I, J, K, 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.221 
• R-Value Work: 0.171 
• R-Value Observed: 0.173 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 197.193	α = 90
b = 99.439	β = 104.45
c = 196.244	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
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