6OJH

Crystal Structure of Haemophilus Influenzae Biotin Carboxylase Complexed with (R)-7-(3-aminopyrrolidin-1-yl)-6-(naphthalen-1-yl)pyrido[2,3-d]pyrimidin-2-amine

• PDB DOI: https://doi.org/10.2210/pdb6OJH/pdb

• Classification: LIGASE
• Organism(s): Haemophilus influenzae Rd KW20
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-04-11 Released: 2020-02-12 
• Deposition Author(s): Andrews, L.D., Kane, T.R., Dozzo, P., Haglund, C.M., Hilderbrandt, D.J., Linsell, M.S., Machajewski, T., McEnroe, G., Serio, A.W., Wlasichuk, K.B., Neau, D.B., Pakhomova, S., Waldrop, G.L., Sharp, M., Pogliano, J., Cirz, R., Cohen, F.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.222 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Haemophilus Influenzae Biotin Carboxylase Complexed with (R)-7-(3-aminopyrrolidin-1-yl)-6-(naphthalen-1-yl)pyrido[2,3-d]pyrimidin-2-amine

Andrews, L.D., Kane, T.R., Dozzo, P., Haglund, C.M., Hilderbrandt, D.J., Linsell, M.S., Machajewski, T., McEnroe, G., Serio, A.W., Wlasichuk, K.B., Neau, D.B., Pakhomova, S., Waldrop, G.L., Sharp, M., Pogliano, J., Cirz, R., Cohen, F.

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

Macromolecule Content

• Total Structure Weight: 51.8 kDa 
• Atom Count: 3,644 
• Modelled Residue Count: 445 
• Deposited Residue Count: 468 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Biotin carboxylase	A	468	Haemophilus influenzae Rd KW20	Mutation(s): 0  Gene Names: accC, HI_0972 EC: 6.3.4.14 (PDB Primary Data), 6.4.1.2 (PDB Primary Data)
UniProt
Find proteins for P43873 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P43873  Go to UniProtKB:  P43873

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MV4	B [auth A]	7-[(3R)-3-aminopyrrolidin-1-yl]-6-(naphthalen-1-yl)pyrido[2,3-d]pyrimidin-2-amine C21 H20 N6 LGFLKSRFTIOLSI-OAHLLOKOSA-N
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.222 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.688	α = 90
b = 85.688	β = 90
c = 104.83	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-02-12 
Deposition Author(s): Andrews, L.D., Kane, T.R., Dozzo, P., Haglund, C.M., Hilderbrandt, D.J., Linsell, M.S., Machajewski, T., McEnroe, G., Serio, A.W., Wlasichuk, K.B., Neau, D.B., Pakhomova, S., Waldrop, G.L., Sharp, M., Pogliano, J., Cirz, R., Cohen, F.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R21AI113572

Revision History  

• Version 1.0: 2020-02-12
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description