3ES4 | pdb_00003es4

Crystal structure of Protein of unknown function (DUF861) with a RmlC-like cupin fold (17741406) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 1.64 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3ES4/pdb

• Classification: structural genomics, unknown function
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-10-03 Released: 2008-10-14 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 
  0.160 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.143 (Depositor) 

Literature

Crystal structure of Protein of unknown function (DUF861) with a RmlC-like cupin fold (17741406) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 1.64 A resolution

Joint Center for Structural Genomics (JCSG)

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: 26.25 kDa 
• Atom Count: 2,220 
• Modeled Residue Count: 232 
• Deposited Residue Count: 232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein DUF861 with a RmlC-like cupin fold	A, B	116	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: 17741406, AGR_L_3519, Atu3045
UniProt
Find proteins for A9CEL1 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CEL1  Go to UniProtKB:  A9CEL1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 1.64 Å
• R-Value Free:  0.160 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.143 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33ES4

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.254	α = 90
b = 95.254	β = 90
c = 83.155	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-14 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-10-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  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: 2024-11-13
  Changes: Data collection, Refinement description, Structure summary