3BGE | pdb_00003bge

Crystal structure of the C-terminal fragment of AAA+ATPase from Haemophilus influenzae

• PDB DOI: https://doi.org/10.2210/pdb3BGE/pdb

• Classification: NUCLEOTIDE BINDING PROTEIN
• Organism(s): Haemophilus influenzae 86-028NP
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-11-26 Released: 2008-01-01 
• Deposition Author(s): Ramagopal, U.A., Patskovsky, Y., Bonanno, J.B., Meyer, A.J., Toro, R., Freeman, J., Adams, J., Koss, J., Maletic, M., Gheyi, T., 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: 1.85 Å
• R-Value Free: 
  0.240 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the C-terminal fragment of AAA+ATPase from Haemophilus influenzae.

Ramagopal, U.A., Patskovsky, Y., Bonanno, J.B., Meyer, A.J., Toro, R., Freeman, J., Adams, J., Koss, J., Maletic, M., Gheyi, T., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 45.64 kDa 
• Atom Count: 2,855 
• Modeled Residue Count: 326 
• Deposited Residue Count: 402 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Predicted ATPase	A, B	201	Haemophilus influenzae 86-028NP	Mutation(s): 1  Gene Names: NTHI1458
UniProt
Find proteins for Q4QL22 (Haemophilus influenzae (strain 86-028NP)) Explore Q4QL22  Go to UniProtKB:  Q4QL22

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.240 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.085	α = 90
b = 93.085	β = 90
c = 83.413	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-01 
Deposition Author(s): Ramagopal, U.A., Patskovsky, Y., Bonanno, J.B., Meyer, A.J., Toro, R., Freeman, J., Adams, J., Koss, J., Maletic, M., Gheyi, T., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-01-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2021-10-20
  Changes: Database references
• Version 1.6: 2023-08-30
  Changes: Data collection, Refinement description