2IN5 | pdb_00002in5

Crystal Structure of the hypothetical lipoprotein YmcC from Escherichia coli (K12), Northeast Structural Genomics target ER552.

PDB DOI: https://doi.org/10.2210/pdb2IN5/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-10-05 Released: 2006-11-07
Deposition Author(s): Zhou, W., Forouhar, F., Seetharaman, J., Chen, C.X., Cunningham, K., Ma, L.-C., Janjua, H., Xiao, R., Baran, M.C., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.256 (Depositor), 0.266 (DCC)
R-Value Work:
0.215 (Depositor), 0.221 (DCC)
R-Value Observed:
0.215 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of the hypothetical lipoprotein YmcC from Escherichia coli (K12), Northeast Structural Genomics target ER552.

Zhou, W., Forouhar, F., Seetharaman, J., Chen, C.X., Cunningham, K., Ma, L.-C., Janjua, H., Xiao, R., Baran, M.C., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

To be published.

Macromolecule Content

Total Structure Weight: 48.05 kDa
Atom Count: 3,285
Modeled Residue Count: 383
Deposited Residue Count: 414
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical lipoprotein ymcC	A, B	207	Escherichia coli K-12	Mutation(s): 5 Gene Names: ymcC, b0986
UniProt
Find proteins for P75884 (Escherichia coli (strain K12)) Explore P75884 Go to UniProtKB: P75884
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P75884
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: 2.30 Å
R-Value Free: 0.256 (Depositor), 0.266 (DCC)
R-Value Work: 0.215 (Depositor), 0.221 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.793	α = 90
b = 74.998	β = 127.11
c = 80.201	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-11-07

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2006-11-07
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: 2024-10-09
Changes: Data collection, Database references, Derived calculations, Structure summary