3ESM | pdb_00003esm

Crystal structure of an uncharacterized protein from Nocardia farcinica reveals an immunoglobulin-like fold

• PDB DOI: https://doi.org/10.2210/pdb3ESM/pdb

• Classification: structural genomics, unknown function
• Organism(s): Nocardia farcinica
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2008-10-06 Released: 2008-10-14 
• Deposition Author(s): Bonanno, J.B., Freeman, J., Bain, K.T., Hu, S., Romero, R., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.262 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.237 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Literature

Crystal structure of an uncharacterized protein from Nocardia farcinica reveals an immunoglobulin-like fold

Bonanno, J.B., Freeman, J., Bain, K.T., Hu, S., Romero, R., Wasserman, S., Sauder, J.M., Burley, S.K., 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)

Macromolecule Content 

• Total Structure Weight: 16.29 kDa 
• Atom Count: 1,164 
• Modeled Residue Count: 138 
• Deposited Residue Count: 152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein	A	152	Nocardia farcinica	Mutation(s): 3  Gene Names: NFA_1110
UniProt
Find proteins for Q5Z3N8 (Nocardia farcinica (strain IFM 10152)) Explore Q5Z3N8  Go to UniProtKB:  Q5Z3N8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SNN	A	L-PEPTIDE LINKING	C4 H6 N2 O2		ASN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.262 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.237 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.582	α = 90
b = 67.582	β = 90
c = 62.571	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-14 
Deposition Author(s): Bonanno, J.B., Freeman, J., Bain, K.T., Hu, S., Romero, R., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-10-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Advisory, Refinement description
• Version 1.3: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2021-10-20
  Changes: Advisory, Database references
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 3.0: 2024-02-07
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
• Version 3.1: 2024-11-20
  Changes: Structure summary