3IBM | pdb_00003ibm

CRYSTAL STRUCTURE OF cupin 2 domain-containing protein Hhal_0468 FROM Halorhodospira halophila

• PDB DOI: https://doi.org/10.2210/pdb3IBM/pdb

• Classification: structural genomics, unknown function
• Organism(s): Halorhodospira halophila SL1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-16 Released: 2009-07-28 
• Deposition Author(s): Patskovsky, Y., Toro, R., Freeman, J., Miller, 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: 2.00 Å
• R-Value Free: 
  0.258 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

CRYSTAL STRUCTURE OF cupin 2 domain-containing PROTEIN Hhal_0468 FROM Halorhodospira halophila

Patskovsky, Y., Toro, R., Freeman, J., Miller, 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: 38.33 kDa 
• Atom Count: 2,534 
• Modeled Residue Count: 291 
• Deposited Residue Count: 334 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cupin 2, conserved barrel domain protein	A, B	167	Halorhodospira halophila SL1	Mutation(s): 0  Gene Names: Hhal_0468
UniProt
Find proteins for A1WU94 (Halorhodospira halophila (strain DSM 244 / SL1)) Explore A1WU94  Go to UniProtKB:  A1WU94

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K	D [auth A], F [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.258 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.791	α = 90
b = 51.734	β = 90
c = 117.784	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-28 
Deposition Author(s): Patskovsky, Y., Toro, R., Freeman, J., Miller, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references