3FIF | pdb_00003fif

Crystal structure of the ygdR protein from E.coli. Northeast Structural Genomics target ER382A.

PDB DOI: https://doi.org/10.2210/pdb3FIF/pdb

Classification: structural genomics, unknown function
Organism(s): Escherichia coli K-12, Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-12-11 Released: 2009-01-06
Deposition Author(s): Kuzin, A.P., Su, M., Seetharaman, J., Rossi, P., Chen, C.X., Jiang, M., Cunningham, K., Ma, L., Xiao, R., Liu, J.C., Baran, M., Swapna, G.V.T., Acton, T.B., Rost, 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:
0.253 (Depositor), 0.251 (DCC)
R-Value Work:
0.238 (Depositor), 0.237 (DCC)
R-Value Observed:
0.239 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of the ygdR protein from E.coli. Northeast Structural Genomics target ER382A.

Kuzin, A.P., Su, M., Seetharaman, J., Rossi, P., Chen, C.X., Jiang, M., Cunningham, K., Ma, L., Xiao, R., Liu, J.C., Baran, M., Swapna, G.V.T., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 58.33 kDa
Atom Count: 3,649
Modeled Residue Count: 452
Deposited Residue Count: 495
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized lipoprotein ygdR	A, B, C, D, E A, B, C, D, E, F, G, H	61	Escherichia coli K-12	Mutation(s): 0 Gene Names: ygdR, b2833, JW2801
UniProt
Find proteins for P65294 (Escherichia coli (strain K12)) Explore P65294 Go to UniProtKB: P65294
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P65294
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized ligand	I [auth Y]	7	Escherichia coli	Mutation(s): 0

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, G, H	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: 0.253 (Depositor), 0.251 (DCC)
R-Value Work: 0.238 (Depositor), 0.237 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.017	α = 99.95
b = 41.056	β = 102.33
c = 73.748	γ = 104.4

Software Package:

Software Name	Purpose
ADSC	data collection
BALBES	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-01-06

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2009-01-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-11-22
Changes: Data collection
Version 1.4: 2024-11-20
Changes: Structure summary