2HUJ | pdb_00002huj

Crystal structure of a protein of uknown function (NP_471338.1) from Listeria innocua at 1.74 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2HUJ/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Listeria innocua
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-07-26 Released: 2006-08-08 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 
  0.207 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

Crystal structures of MW1337R and lin2004: representatives of a novel protein family that adopt a four-helical bundle fold.

Kozbial, P., Xu, Q., Chiu, H.J., McMullan, D., Krishna, S.S., Miller, M.D., Abdubek, P., Acosta, C., Astakhova, T., Axelrod, H.L., Carlton, D., Clayton, T., Deller, M., Duan, L., Elias, Y., Elsliger, M.A., Feuerhelm, J., Grzechnik, S.K., Hale, J., Han, G.W., Jaroszewski, L., Jin, K.K., Klock, H.E., Knuth, M.W., Koesema, E., Kumar, A., Marciano, D., Morse, A.T., Murphy, K.D., Nigoghossian, E., Okach, L., Oommachen, S., Reyes, R., Rife, C.L., Spraggon, G., Trout, C.V., van den Bedem, H., Weekes, D., White, A., Wolf, G., Zubieta, C., Hodgson, K.O., Wooley, J., Deacon, A.M., Godzik, A., Lesley, S.A., Wilson, I.A.

(2008) Proteins 71: 1589-1596

• PubMed: 18324683 
• DOI: https://doi.org/10.1002/prot.22020
• Primary Citation Related Structures: 
  2ETS, 2HUJ

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Organizational Affiliation: 
• Joint Center for Structural Genomics, La Jolla, California, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 17.22 kDa 
• Atom Count: 1,153 
• Modeled Residue Count: 125 
• Deposited Residue Count: 140 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lin2004 protein	A	140	Listeria innocua	Mutation(s): 4  Gene Names: NP_471338.1
UniProt
Find proteins for Q92AB8 (Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)) Explore Q92AB8  Go to UniProtKB:  Q92AB8

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free:  0.207 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32HUJ

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.11	α = 90
b = 100.11	β = 90
c = 66.916	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-08 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2006-08-08
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-13
  Changes: Data collection, Structure summary