1Y89 | pdb_00001y89

Crystal Structure of devB protein

• PDB DOI: https://doi.org/10.2210/pdb1Y89/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-12-10 Released: 2005-01-25 
• Deposition Author(s): Lazarski, K., Cymborowski, M., Chruszcz, M., Zheng, H., Zhang, R., Lezondra, L., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.194 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Literature

Crystal Structure of devB protein

Lazarski, K., Cymborowski, M., Chruszcz, M., Zheng, H., Zhang, R., Lezondra, L., Joachimiak, A., Minor, W.

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.

Macromolecule Content 

• Total Structure Weight: 54.02 kDa 
• Atom Count: 4,334 
• Modeled Residue Count: 476 
• Deposited Residue Count: 476 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
devB protein	A, B	238	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 5  EC: 3.1.1.31
UniProt
Find proteins for Q9KL51 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KL51  Go to UniProtKB:  Q9KL51

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2PE	J [auth B]	NONAETHYLENE GLYCOL C18 H38 O10 YZUUTMGDONTGTN-UHFFFAOYSA-N
PE5	F [auth A], K [auth B]	3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL C18 H38 O9 CUDPPTPIUWYGFI-UHFFFAOYSA-N
PEG	L [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4	C [auth A], D [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.194 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.078	α = 90
b = 85.078	β = 90
c = 181.08	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	model building
RESOLVE	model building
REFMAC	refinement
SCALEPACK	data scaling
DM	phasing
RESOLVE	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-25 
Deposition Author(s): Lazarski, K., Cymborowski, M., Chruszcz, M., Zheng, H., Zhang, R., Lezondra, L., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2005-01-25
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary