3RCM | pdb_00003rcm

crystal structure of EFI target 500140:TatD family hydrolase from Pseudomonas putida

• PDB DOI: https://doi.org/10.2210/pdb3RCM/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas putida KT2440
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-03-31 Released: 2011-04-20 
• Deposition Author(s): Kim, J., Toro, R., Hillerich, B., Seidel, R.D., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.226 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.172 (Depositor) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

crystal structure of EFI target 500140:TatD family hydrolase from Pseudomonas putida

Kim, J., Toro, R., Hillerich, B., Seidel, R.D., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 32.73 kDa 
• Atom Count: 2,339 
• Modeled Residue Count: 279 
• Deposited Residue Count: 287 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TatD family hydrolase	A	287	Pseudomonas putida KT2440	Mutation(s): 0  Gene Names: PP2311, PP_2311 EC: 3.1.21
UniProt
Find proteins for Q88KH9 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88KH9  Go to UniProtKB:  Q88KH9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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: 2.05 Å
• R-Value Free:  0.226 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.172 (Depositor) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.007	α = 90
b = 62.643	β = 90
c = 88.57	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-20 
Deposition Author(s): Kim, J., Toro, R., Hillerich, B., Seidel, R.D., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2011-04-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary