5HQH | pdb_00005hqh

1.32 Angstrom Crystal Structure of Ybbr like Domain of lmo2119 Protein from Listeria monocytogenes.

• PDB DOI: https://doi.org/10.2210/pdb5HQH/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Listeria monocytogenes EGD-e
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-01-21 Released: 2016-02-03 
• Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Winsor, J., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 
  0.192 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.162 (Depositor) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

1.32 Angstrom Crystal Structure of Ybbr like Domain of lmo2119 Protein from Listeria monocytogenes.

Minasov, G., Shuvalova, L., Dubrovska, I., Winsor, J., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 12.04 kDa 
• Atom Count: 1,064 
• Modeled Residue Count: 96 
• Deposited Residue Count: 109 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lmo2119 protein	A	109	Listeria monocytogenes EGD-e	Mutation(s): 0  Gene Names: lmo2119
UniProt
Find proteins for Q8Y5E5 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y5E5  Go to UniProtKB:  Q8Y5E5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free:  0.192 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.162 (Depositor) 
• R-Value Observed: 0.164 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35hqh

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 22.577	α = 90
b = 28.819	β = 95.65
c = 59.733	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-03 
Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Winsor, J., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2016-02-03
  Type: Initial release
  
• Version 1.1: 2016-03-02
  Changes: Structure summary
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary