2HJ1 | pdb_00002hj1

Crystal structure of a 3D domain-swapped dimer of protein HI0395 from Haemophilus influenzae

• PDB DOI: https://doi.org/10.2210/pdb2HJ1/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Haemophilus influenzae 86-028NP
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-06-29 Released: 2006-08-29 
• Deposition Author(s): Ramagopal, U.A., Patskovsky, Y.V., Toro, R., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.231 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Literature

Crystal structure of a 3D domain-swapped dimer of hypothetical protein from Haemophilus influenzae (CASP Target)

Ramagopal, U.A., Patskovsky, Y.V., Toro, R., 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)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 22.84 kDa 
• Atom Count: 1,419 
• Modeled Residue Count: 157 
• Deposited Residue Count: 194 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A, B	97	Haemophilus influenzae 86-028NP	Mutation(s): 0
UniProt
Find proteins for P43994 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Go to UniProtKB:  P43994
Find proteins for Q4QNE7 (Haemophilus influenzae (strain 86-028NP)) Explore Q4QNE7  Go to UniProtKB:  Q4QNE7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth B], E [auth B], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.231 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.381	α = 90
b = 74.381	β = 90
c = 117.027	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SHELXD	phasing
SHELXE	model building
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-29 
Deposition Author(s): Ramagopal, U.A., Patskovsky, Y.V., Toro, R., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2006-08-29
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-14
  Changes: Data collection, Database references