3LYV | pdb_00003lyv

Crystal structure of a domain of ribosome-associated factor Y from streptococcus pyogenes serotype M6. Northeast Structural Genomics Consortium target id DR64A

PDB DOI: https://doi.org/10.2210/pdb3LYV/pdb

Classification: CHAPERONE
Organism(s): Streptococcus pyogenes serotype M6
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-02-28 Released: 2010-05-26
Deposition Author(s): Seetharaman, J., Neely, H., Forouhar, F., Wang, D., Janjua, H., Cunningham, K., Owens, L., 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: 2.70 Å
R-Value Free:
0.284 (Depositor), 0.294 (DCC)
R-Value Work:
0.244 (Depositor), 0.257 (DCC)
R-Value Observed:
0.244 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of a domain of ribosome-associated factor Y from streptococcus pyogenes serotype M6. Northeast Structural Genomics Consortium target id DR64A

Seetharaman, J., Neely, H., Forouhar, F., Wang, D., Janjua, H., Cunningham, K., Owens, L., 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: 47.43 kDa
Atom Count: 2,599
Modeled Residue Count: 321
Deposited Residue Count: 396
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome-associated factor Y	A, B, C, D, E A, B, C, D, E, F	66	Streptococcus pyogenes serotype M6	Mutation(s): 0 Gene Names: M6_Spy1371
UniProt
Find proteins for Q5XAQ7 (Streptococcus pyogenes serotype M6 (strain ATCC BAA-946 / MGAS10394)) Explore Q5XAQ7 Go to UniProtKB: Q5XAQ7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5XAQ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	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: 0.284 (Depositor), 0.294 (DCC)
R-Value Work: 0.244 (Depositor), 0.257 (DCC)
R-Value Observed: 0.244 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.602	α = 90
b = 64.677	β = 96.6
c = 69.563	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-05-26

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2010-05-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary