5DN8 | pdb_00005dn8

1.76 Angstrom Crystal Structure of GTP-binding Protein Der from Coxiella burnetii in Complex with GDP.

• PDB DOI: https://doi.org/10.2210/pdb5DN8/pdb

• Classification: GTP-binding protein
• Organism(s): Coxiella burnetii RSA 493
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2015-09-09 Released: 2015-10-14 
• Deposition Author(s): Minasov, G., Shuvalova, L., Han, A., Kim, H.-Y., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.204 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

1.76 Angstrom Crystal Structure of GTP-binding Protein Der from Coxiella burnetii in Complex with GDP.

Minasov, G., Shuvalova, L., Han, A., Kim, H.-Y., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 50.94 kDa 
• Atom Count: 3,937 
• Modeled Residue Count: 405 
• Deposited Residue Count: 446 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase Der	A	446	Coxiella burnetii RSA 493	Mutation(s): 0  Gene Names: der, engA, CBU_1245
UniProt
Find proteins for Q83C83 (Coxiella burnetii (strain RSA 493 / Nine Mile phase I)) Explore Q83C83  Go to UniProtKB:  Q83C83

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	B [auth A], C [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.204 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35dn8

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.275	α = 90
b = 98.443	β = 90
c = 107.968	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
BLU-MAX	data collection
HKL-2000	data scaling
PHASER	phasing
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-14 
Deposition Author(s): Minasov, G., Shuvalova, L., Han, A., Kim, H.-Y., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2015-10-14
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description