5J7M | pdb_00005j7m

Crystal structure of Cupin 2 conserved barrel domain protein from Kribbella flavida DSM 17836

• PDB DOI: https://doi.org/10.2210/pdb5J7M/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Kribbella flavida DSM 17836
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2016-04-06 Released: 2016-04-27 
• Deposition Author(s): Chang, C., Cuff, M., Chhor, G., Endres, M., Joachimiak, A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 
  0.224 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Crystal structure of Cupin 2 conserved barrel domain protein from Kribbella flavida DSM 17836

Chang, C., Cuff, M., Chhor, G., Endres, M., Joachimiak, A.

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)

Macromolecule Content 

• Total Structure Weight: 27.82 kDa 
• Atom Count: 1,979 
• Modeled Residue Count: 244 
• Deposited Residue Count: 246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cupin 2 conserved barrel domain protein	A, B	123	Kribbella flavida DSM 17836	Mutation(s): 0  Gene Names: Kfla_2934
UniProt
Find proteins for D2Q1L0 (Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399)) Explore D2Q1L0  Go to UniProtKB:  D2Q1L0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	E [auth A], F [auth A], J [auth B], K [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ACT	G [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NI	D [auth A], I [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
EOH	C [auth A], H [auth B]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free:  0.224 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.162	α = 90
b = 61.162	β = 90
c = 120.973	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-04-27 
Deposition Author(s): Chang, C., Cuff, M., Chhor, G., Endres, M., Joachimiak, A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM115586

Revision History  

• Version 1.0: 2016-04-27
  Type: Initial release
  
• Version 1.1: 2016-08-17
  Changes: Database references, Structure summary
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary