2O8S | pdb_00002o8s

X-ray Crystal Structure of Protein AGR_C_984 from Agrobacterium tumefaciens. Northeast Structural Genomics Consortium Target AtR120.

PDB DOI: https://doi.org/10.2210/pdb2O8S/pdb

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

Deposited: 2006-12-12 Released: 2007-01-30
Deposition Author(s): Seetharaman, J., Forouhar, F., Su, M., Zhao, L., Cunningham, K., Ma, L.-C., Janjua, H., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.279 (Depositor), 0.273 (DCC)
R-Value Work:
0.243 (Depositor), 0.271 (DCC)
R-Value Observed:
0.243 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of the Hypothetical Protein AGR_C_984 from Agrobacterium tumefaciens, Northeast Structural Genomics Target AtR120.

Seetharaman, J., Forouhar, F., Su, M., Zhao, L., Cunningham, K., Ma, L.-C., Janjua, H., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 70.84 kDa
Atom Count: 3,650
Modeled Residue Count: 460
Deposited Residue Count: 646
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AGR_C_984p	A, B	323	Agrobacterium fabrum str. C58	Mutation(s): 6 Gene Names: locus_tag="AGR_C_984"
UniProt
Find proteins for Q7D182 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7D182 Go to UniProtKB: Q7D182
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7D182
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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: 2.40 Å
R-Value Free: 0.279 (Depositor), 0.273 (DCC)
R-Value Work: 0.243 (Depositor), 0.271 (DCC)
R-Value Observed: 0.243 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.49	α = 90
b = 42.49	β = 90
c = 332.804	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SOLVE	phasing
XTALVIEW	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-01-30

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2007-01-30
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2019-08-14
Changes: Data collection
Version 1.5: 2023-12-27
Changes: Data collection, Database references, Derived calculations
Version 1.6: 2024-11-13
Changes: Structure summary