4LMI | pdb_00004lmi

Crystal structure of putative ketosteroid isomerase from Kribbella flavida DSM 17836

• PDB DOI: https://doi.org/10.2210/pdb4LMI/pdb

• Classification: Structural genomics, unknown function
• Organism(s): Kribbella flavida DSM 17836
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-07-10 Released: 2013-07-31 
• Deposition Author(s): Chang, C., Chhor, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Literature

Crystal structure of putative ketosteroid isomerase from Kribbella flavida DSM 17836

Chang, C., 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: 32.01 kDa 
• Atom Count: 2,529 
• Modeled Residue Count: 271 
• Deposited Residue Count: 278 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	139	Kribbella flavida DSM 17836	Mutation(s): 0  Gene Names: Kfla_6894
UniProt
Find proteins for D2Q2I7 (Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399)) Explore D2Q2I7  Go to UniProtKB:  D2Q2I7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	C [auth A], D [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-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: 1.80 Å
• R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.536	α = 90
b = 69.873	β = 90
c = 94.809	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXDE	phasing
RESOLVE	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-31 
Deposition Author(s): Chang, C., Chhor, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2013-07-31
  Type: Initial release
  
• Version 1.1: 2013-08-21
  Changes: Database references, Structure summary
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary