4PVB | pdb_00004pvb

Crystal structure of Aminopeptidase N in complex with the phosphonic acid analogue of leucine (D-(S)-LeuP)

• PDB DOI: https://doi.org/10.2210/pdb4PVB/pdb

• Classification: HYDROLASE
• Organism(s): Neisseria meningitidis MC58
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-03-16 Released: 2014-06-25 
• Deposition Author(s): Nocek, B., Vassiliou, S., Berlicki, L., Mulligan, R., Mucha, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.233 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Aminopeptidase N in complex with the phosphonic acid analogue of leucine (D-(S)-LeuP)

Nocek, B., Vassiliou, S., Mulligan, R., Weglarz-Tomczak, E., Berlicki, L., Pawelczak, M., Mucha, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 99.5 kDa 
• Atom Count: 7,259 
• Modeled Residue Count: 864 
• Deposited Residue Count: 867 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminopeptidase N	A	867	Neisseria meningitidis MC58	Mutation(s): 0  Gene Names: pepN, NMB1416 EC: 3.4.11.2
UniProt
Find proteins for Q9JYV4 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58)) Explore Q9JYV4  Go to UniProtKB:  Q9JYV4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2WW	B [auth A]	[(1S)-1-amino-3-methylbutyl]phosphonic acid C5 H14 N O3 P HGCAUCAWEADMPM-YFKPBYRVSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
PO4	I [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.233 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 224.264	α = 90
b = 224.264	β = 90
c = 57.943	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
MOLREP	phasing
CCP4	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-25 
Deposition Author(s): Nocek, B., Vassiliou, S., Berlicki, L., Mulligan, R., Mucha, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2014-06-25
  Type: Initial release
  
• Version 1.1: 2020-05-13
  Changes: Derived calculations, Structure summary
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection
• Version 1.4: 2024-10-30
  Changes: Structure summary