2IT9 | pdb_00002it9

Crystal structure of a protein with unknown function from DUF155 family (YP_292156.1) from Prochlorococcus sp. NATL2A at 1.80 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2IT9/pdb

• Classification: Structural Genomics/Unknown function
• Organism(s): Prochlorococcus marinus str. NATL2A
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-10-19 Released: 2006-11-28 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.213 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Crystal structure of hypothetical protein (YP_292156.1) from Prochlorococcus sp. NATL2A at 1.80 A resolution

Joint Center for Structural Genomics (JCSG)

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.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 61.04 kDa 
• Atom Count: 4,474 
• Modeled Residue Count: 482 
• Deposited Residue Count: 508 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A, B, C, D	127	Prochlorococcus marinus str. NATL2A	Mutation(s): 5  Gene Names: YP_292156.1
UniProt
Find proteins for Q46J75 (Prochlorococcus marinus (strain NATL2A)) Explore Q46J75  Go to UniProtKB:  Q46J75

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	F [auth A], G [auth B], K [auth D]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
TRS	M [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
EDO	H [auth B], I [auth C], J [auth C], L [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 1.80 Å
• R-Value Free:  0.213 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32IT9

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.723	α = 90
b = 81.021	β = 90
c = 124.352	γ = 90

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
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-28 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2006-11-28
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Advisory, Refinement description
• Version 1.4: 2017-10-25
  Changes: Author supporting evidence
• Version 1.5: 2023-01-25
  Changes: Advisory, Database references, Derived calculations
• Version 1.6: 2024-11-06
  Changes: Data collection, Refinement description, Structure summary