4L0C | pdb_00004l0c

Crystal structure of the N-Fopmylmaleamic acid deformylase Nfo(S94A) from Pseudomonas putida S16

• PDB DOI: https://doi.org/10.2210/pdb4L0C/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas putida S16
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-05-31 Released: 2014-06-04 
• Deposition Author(s): Chen, D., Lu, Y., Zhang, Z., Wu, G., Xu, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.211 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

Crystal structure of the N-Fopmylmaleamic acid deformylase Nfo from Pseudomonas putida S16

Chen, D., Lu, Y., Zhang, Z., Wu, G., Xu, P.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Biological Assembly 7  

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

Biological assembly 7 assigned by authors.

Biological Assembly 8  

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

Biological assembly 8 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 228.65 kDa 
• Atom Count: 18,024 
• Modeled Residue Count: 2,029 
• Deposited Residue Count: 2,040 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deformylase	A, B, C, D, E, F, G, H	255	Pseudomonas putida S16	Mutation(s): 1  Gene Names: PPS_4059
UniProt
Find proteins for F8G0M2 (Pseudomonas putida (strain DSM 28022 / S16)) Explore F8G0M2  Go to UniProtKB:  F8G0M2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	S [auth H]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ACY	I [auth A], J [auth A], K [auth B], L [auth C], M [auth D], N [auth E], O [auth F], P [auth G], Q [auth G], R [auth H]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.211 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.412	α = 90
b = 87.268	β = 94.42
c = 130.879	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-04 
Deposition Author(s): Chen, D., Lu, Y., Zhang, Z., Wu, G., Xu, P.

Revision History  

• Version 1.0: 2014-06-04
  Type: Initial release
  
• Version 1.1: 2016-12-21
  Changes: Structure summary
• Version 1.2: 2016-12-28
  Changes: Database references
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary