4YF1 | pdb_00004yf1

1.85 angstrom crystal structure of lmo0812 from Listeria monocytogenes EGD-e

• PDB DOI: https://doi.org/10.2210/pdb4YF1/pdb

• Classification: HYDROLASE
• Organism(s): Listeria monocytogenes EGD-e
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-02-24 Released: 2015-03-04 
• Deposition Author(s): Krishna, S.N., Light, S.H., Filippova, E.V., Minasov, G., Kiryukhina, O., Jedrzejczak, R., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.208 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

1.85 angstrom crystal structure of lmo0812 from Listeria monocytogenes EGD-e

Krishna, S.N., Light, S.H., Filippova, E.V., Minasov, G., Kiryukhina, O., Jedrzejczak, R., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

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: 88.42 kDa 
• Atom Count: 5,635 
• Modeled Residue Count: 614 
• Deposited Residue Count: 748 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lmo0812 protein	A, B, C, D	187	Listeria monocytogenes EGD-e	Mutation(s): 0  Gene Names: lmo0812
UniProt
Find proteins for Q8Y8T2 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y8T2  Go to UniProtKB:  Q8Y8T2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	F [auth B]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
NA	E [auth A], G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-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: 1.85 Å
• R-Value Free:  0.208 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.811	α = 90
b = 58.675	β = 114.31
c = 95.73	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-04 
Deposition Author(s): Krishna, S.N., Light, S.H., Filippova, E.V., Minasov, G., Kiryukhina, O., Jedrzejczak, R., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2015-03-04
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary