3QME | pdb_00003qme

Crystal Structure of an Anopheles gambiae Odorant-binding Protein AgamOBP22a with Bound Odorant Cyclohexanone

• PDB DOI: https://doi.org/10.2210/pdb3QME/pdb
• Entry: 3QME supersedes: 3L5G

• Classification: TRANSPORT PROTEIN
• Organism(s): Anopheles gambiae str. PEST
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-02-04 Released: 2011-02-23 
• Deposition Author(s): Ren, H., Zhang, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Crystal Structures of an Anopheles gambiae Odorant-binding Protein AgamOBP22a and Complexes with Bound Odorants

Ren, H., Yang, G., Winberg, G., Turin, L., Zhang, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 16.21 kDa 
• Atom Count: 1,064 
• Modeled Residue Count: 119 
• Deposited Residue Count: 141 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Odorant binding protein (AGAP010409-PA)	A	141	Anopheles gambiae str. PEST	Mutation(s): 0  Gene Names: AgamOBP22a, AGAP010409, OBP22, OBPjj83b
UniProt
Find proteins for Q7PGA3 (Anopheles gambiae) Explore Q7PGA3  Go to UniProtKB:  Q7PGA3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CYH	B [auth A]	CYCLOHEXANONE C6 H10 O JHIVVAPYMSGYDF-UHFFFAOYSA-N
NH4	C [auth A], D [auth A], E [auth A], F [auth A]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.986	α = 90
b = 37.593	β = 99.17
c = 43.618	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-23 
Deposition Author(s): Ren, H., Zhang, S.
• This entry supersedes: 3L5G

Revision History  

• Version 1.0: 2011-02-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2018-03-07
  Changes: Data collection
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-09
  Changes: Structure summary