4U13 | pdb_00004u13

Crystal structure of putative polyketide cyclase (protein SMa1630) from Sinorhizobium meliloti at 2.3 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4U13/pdb

• Classification: TRANSFERASE
• Organism(s): Sinorhizobium meliloti 1021
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-07-14 Released: 2014-09-10 
• Deposition Author(s): Shabalin, I.G., Bacal, P., Osinski, T., Cooper, D.R., Szlachta, K., Stead, M., Grabowski, M., Hammonds, J., Ahmed, M., Hillerich, B.S., Bonanno, J., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)
• 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: 2.30 Å
• R-Value Free: 
  0.224 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a putative polyketide cyclase (protein SMa1630) from Sinorhizobium meliloti at 2.3 A resolution

Shabalin, I.G., Bacal, P., Osinski, T., Cooper, D.R., Szlachta, K., Stead, M., Grabowski, M., Hammonds, J., Ahmed, M., Hillerich, B.S., Bonanno, J., Seidel, R., Almo, S.C., Minor, W.

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: 24.06 kDa 
• Atom Count: 1,656 
• Modeled Residue Count: 218 
• Deposited Residue Count: 218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative polyketide cyclase SMa1630	A, B	109	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: SMa1630
UniProt
Find proteins for Q92YJ1 (Rhizobium meliloti (strain 1021)) Explore Q92YJ1  Go to UniProtKB:  Q92YJ1

Small Molecules

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: 2.30 Å
• R-Value Free:  0.224 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M3DS3Q

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.764	α = 90
b = 42.295	β = 111.83
c = 62.287	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	phasing
HKL-3000	data scaling
PHENIX	phasing
REFMAC	refinement
Coot	model building
PDB_EXTRACT	data extraction
SCALEPACK	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-09-10 
Deposition Author(s): Shabalin, I.G., Bacal, P., Osinski, T., Cooper, D.R., Szlachta, K., Stead, M., Grabowski, M., Hammonds, J., Ahmed, M., Hillerich, B.S., Bonanno, J., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	NIH-5U54GM094662-04

Revision History  

• Version 1.0: 2014-09-10
  Type: Initial release
  
• Version 1.1: 2014-09-24
  Changes: Refinement description, Structure summary
• Version 1.2: 2015-08-26
  Changes: Data collection
• Version 1.3: 2017-09-20
  Changes: Author supporting evidence, Derived calculations, Refinement description
• Version 1.4: 2019-12-25
  Changes: Author supporting evidence
• Version 1.5: 2022-04-13
  Changes: Database references, Structure summary
• Version 1.6: 2023-09-27
  Changes: Data collection, Refinement description
• Version 1.7: 2023-11-15
  Changes: Data collection
• Version 1.8: 2024-10-30
  Changes: Structure summary