5ZCA | pdb_00005zca

Crystal structure of lambda repressor (1-20) fused with maltose-binding protein

• PDB DOI: https://doi.org/10.2210/pdb5ZCA/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Lambdavirus lambda, Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-02-16 Released: 2018-08-15 
• Deposition Author(s): Hanazono, Y., Takeda, K., Miki, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.215 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.173 (Depositor) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Co-translational folding of alpha-helical proteins: structural studies of intermediate-length variants of the lambda repressor

Hanazono, Y., Takeda, K., Miki, K.

(2018) FEBS Open Bio 8: 1312-1321

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 43.56 kDa 
• Atom Count: 3,467 
• Modeled Residue Count: 383 
• Deposited Residue Count: 391 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Repressor protein cI,Maltose-binding periplasmic protein	A	391	Lambdavirus lambda, Escherichia coli K-12 This entity is chimeric	Mutation(s): 0  Gene Names: cI, lambdap88, malE, b4034, JW3994
UniProt
Find proteins for P03034 (Escherichia phage lambda) Explore P03034  Go to UniProtKB:  P03034
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
UniProt Groups	P03034P0AEX9

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	B	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.215 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.173 (Depositor) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.956	α = 90
b = 58.343	β = 90
c = 124.609	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-15 
Deposition Author(s): Hanazono, Y., Takeda, K., Miki, K.

Revision History  

• Version 1.0: 2018-08-15
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary