4M6D | pdb_00004m6d

Crystal structure of the aptamer minF-lysozyme complex.

• PDB DOI: https://doi.org/10.2210/pdb4M6D/pdb
• NAKB: 4M6D

• Classification: Hydrolase/RNA
• Organism(s): Gallus gallus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-08-09 Released: 2013-12-11 
• Deposition Author(s): Malashkevich, V.N., Padlan, F.C., Toro, R., Girvin, M., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free: 
  0.216 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the aptamer minF-lysozyme complex.

Malashkevich, V.N., Padlan, F.C., Toro, R., Girvin, M., Almo, S.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 173.12 kDa 
• Atom Count: 11,432 
• Modeled Residue Count: 1,024 
• Deposited Residue Count: 1,044 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A, C, E, G, I, K	129	Gallus gallus	Mutation(s): 0  Gene Names: LYZ, lyz1 EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Entity ID: 2
Molecule	Chains	Length	Organism	Image
aptamer	B, D, F, H, J, L	45	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free:  0.216 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.914	α = 118.59
b = 132.289	β = 96.39
c = 131.539	γ = 96.27

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-11 
Deposition Author(s): Malashkevich, V.N., Padlan, F.C., Toro, R., Girvin, M., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2013-12-11
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Advisory, Database references, Structure summary
• Version 1.2: 2023-09-20
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-27
  Changes: Structure summary