5MLG | pdb_00005mlg

Crystal structure of rat prorenin

• PDB DOI: https://doi.org/10.2210/pdb5MLG/pdb

• Classification: HYDROLASE
• Organism(s): Rattus norvegicus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2016-12-06 Released: 2017-12-20 
• Deposition Author(s): Yan, Y., Read, R.
• Funding Organization(s): Wellcome Trust, British Heart Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.230 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of rat prorenin

Yan, Y., Zhou, A., Read, R.J.

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: 43.1 kDa 
• Atom Count: 2,827 
• Modeled Residue Count: 364 
• Deposited Residue Count: 389 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Renin	A	389	Rattus norvegicus	Mutation(s): 0  Gene Names: Ren1, Ren EC: 3.4.23.15
UniProt
Find proteins for P08424 (Rattus norvegicus) Explore P08424  Go to UniProtKB:  P08424
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P08424-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.230 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.543	α = 90
b = 142.543	β = 90
c = 77.035	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): Yan, Y., Read, R.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	082961/Z/07/Z
British Heart Foundation	United Kingdom	PG/12/41/29679

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-11-06
  Changes: Structure summary