3R09 | pdb_00003r09

Crystal structure of probable HAD family hydrolase from Pseudomonas fluorescens Pf-5 with bound Mg

• PDB DOI: https://doi.org/10.2210/pdb3R09/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas protegens Pf-5
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-03-07 Released: 2011-04-20 
• Deposition Author(s): Vetting, M.W., Patskovsky, Y., Toro, R., Freeman, J., Miller, S., Sauder, J.M., Burley, S.K., Dunaway-Mariano, D., Allen, K.N., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI), New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.208 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of probable HAD family hydrolase from Pseudomonas fluorescens Pf-5 with bound Mg

Vetting, M.W., Patskovsky, Y., Toro, R., Freeman, J., Miller, S., Sauder, J.M., Burley, S.K., Dunaway-Mariano, D., Allen, K.N., Gerlt, J.A., Almo, S.C.

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: 22.89 kDa 
• Atom Count: 1,698 
• Modeled Residue Count: 197 
• Deposited Residue Count: 205 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydrolase, haloacid dehalogenase-like family	A	205	Pseudomonas protegens Pf-5	Mutation(s): 0  Gene Names: PF-5, PFL_5400
UniProt
Find proteins for Q4K5L5 (Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)) Explore Q4K5L5  Go to UniProtKB:  Q4K5L5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.208 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.299	α = 90
b = 66.299	β = 90
c = 251.29	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-20 
Deposition Author(s): Vetting, M.W., Patskovsky, Y., Toro, R., Freeman, J., Miller, S., Sauder, J.M., Burley, S.K., Dunaway-Mariano, D., Allen, K.N., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI), New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2011-04-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-11-16
  Changes: Atomic model
• Version 1.3: 2013-11-20
  Changes: Database references, Structure summary
• Version 1.4: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.5: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.6: 2023-09-13
  Changes: Data collection, Database references, Refinement description
• Version 1.7: 2023-12-06
  Changes: Data collection
• Version 1.8: 2024-10-16
  Changes: Structure summary