3M9L | pdb_00003m9l

Crystal structure of probable had family hydrolase from pseudomonas fluorescens pf-5

• PDB DOI: https://doi.org/10.2210/pdb3M9L/pdb

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


• Deposited: 2010-03-22 Released: 2010-04-07 
• Deposition Author(s): Patskovsky, Y., Toro, R., Freeman, J., Miller, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.211 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

Crystal Structure of Had Family Hydrolase from Pseudomonas Fluorescens Pf-5

Patskovsky, Y., Toro, R., Freeman, J., Miller, S., Sauder, J.M., Burley, S.K., 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: 22.95 kDa 
• Atom Count: 1,934 
• Modeled Residue Count: 201 
• 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: 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 1.60 Å
• R-Value Free:  0.211 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.99	α = 90
b = 65.99	β = 90
c = 249.775	γ = 120

Software Package:

Software Name	Purpose
SHELX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-07 
Deposition Author(s): Patskovsky, Y., Toro, R., Freeman, J., Miller, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Structure summary