3LOC | pdb_00003loc

Crystal structure of putative transcriptional regulator ycdc

• PDB DOI: https://doi.org/10.2210/pdb3LOC/pdb
• Entry: 3LOC supersedes: 1PB6

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


• Deposited: 2010-02-03 Released: 2010-03-16 
• Deposition Author(s): Patskovsky, Y.V., Knapik, A.A., Mennella, V., Burley, S.K., Minor, W., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.229 (Depositor) 
• R-Value Work: 
  0.195 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Literature

Crystal Structure of Hypothetical Transcriptional Regulator Ycdc from Escherichia Coli

Patskovsky, Y.V., Mennella, V., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 96.25 kDa 
• Atom Count: 6,366 
• Modeled Residue Count: 803 
• Deposited Residue Count: 848 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional regulator rutR	A, B, C, D	212	Escherichia coli K-12	Mutation(s): 0  Gene Names: b1013, JW0998, rutR, ycdC
UniProt
Find proteins for P0ACU2 (Escherichia coli (strain K12)) Explore P0ACU2  Go to UniProtKB:  P0ACU2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
URA	E [auth A], F [auth B], G [auth C], H [auth D]	URACIL C4 H4 N2 O2 ISAKRJDGNUQOIC-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.229 (Depositor) 
• R-Value Work:  0.195 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.02	α = 90
b = 139.61	β = 90
c = 156	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SOLVE	phasing
RESOLVE	model building
HKL-3000	phasing
REFMAC	refinement
Coot	model building
DENZO	data reduction
SCALEPACK	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-16 
Deposition Author(s): Patskovsky, Y.V., Knapik, A.A., Mennella, V., Burley, S.K., Minor, W., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)
• This entry supersedes: 1PB6

Revision History  

• Version 1.0: 2010-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-02-10
  Changes: Derived calculations, Structure summary
• Version 1.4: 2022-04-13
  Changes: Database references, Structure summary
• Version 1.5: 2024-10-16
  Changes: Data collection, Structure summary