2NYS | pdb_00002nys

X-ray Crystal Structure of Protein AGR_C_3712 from Agrobacterium tumefaciens. Northeast Structural Genomics Consortium Target AtR88.

PDB DOI: https://doi.org/10.2210/pdb2NYS/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Agrobacterium fabrum str. C58
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-11-21 Released: 2006-12-05
Deposition Author(s): Vorobiev, S.M., Abashidze, M., Seetharaman, J., Zhao, L., Ma, L.C., Cunningham, K., Nwosu, C., Xiao, R., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.268 (Depositor), 0.280 (DCC)
R-Value Work:
0.242 (Depositor), 0.255 (DCC)
R-Value Observed:
0.242 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2NYS

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of the hypothetical protein AGR_C_3712 from Agrobacterium tumefaciens.

Vorobiev, S.M., Abashidze, M., Seetharaman, J., Zhao, L., Ma, L.C., Cunningham, K., Nwosu, C., Acton, T.B., Xiao, R., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 40.36 kDa
Atom Count: 1,870
Modeled Residue Count: 232
Deposited Residue Count: 352
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AGR_C_3712p	A, B	176	Agrobacterium fabrum str. C58	Mutation(s): 5 Gene Names: AGR_C3712
UniProt
Find proteins for Q8U561 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q8U561 Go to UniProtKB: Q8U561
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8U561
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.268 (Depositor), 0.280 (DCC)
R-Value Work: 0.242 (Depositor), 0.255 (DCC)
R-Value Observed: 0.242 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.55	α = 90
b = 137.55	β = 90
c = 57.113	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SnB	phasing
RESOLVE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-12-05

Deposition Author(s):

Seetharaman, J.

Montelione, G.T.

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2006-12-05
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2021-10-20
Changes: Database references, Derived calculations
Version 1.5: 2023-12-27
Changes: Data collection
Version 1.6: 2024-11-13
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.