3GI7 | pdb_00003gi7

Crystal structure of a duf1311 family protein (pp0307) from pseudomonas putida kt2440 at 1.85 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3GI7/pdb

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


• Deposited: 2009-03-05 Released: 2009-03-31 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.199 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

Crystal structure of secreted protein of unknown function (DUF1311) (NP_742474.1) from Pseudomonas putida KT2440 at 1.85 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.08 kDa 
• Atom Count: 1,929 
• Modeled Residue Count: 201 
• Deposited Residue Count: 244 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Secreted protein of unknown function DUF1311	A, B	122	Pseudomonas putida KT2440	Mutation(s): 0  Gene Names: NP_742474.1, PP0307, PP_0307
UniProt
Find proteins for Q88R27 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88R27  Go to UniProtKB:  Q88R27

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
UNL	C [auth A], F [auth B]	Unknown ligand QAOWNCQODCNURD-UHFFFAOYSA-L

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: 1.85 Å
• R-Value Free:  0.199 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33GI7

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.027	α = 90
b = 100.027	β = 90
c = 58.343	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-31 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-03-31
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-06
  Changes: Data collection, Structure summary