3GNL | pdb_00003gnl

Structure of uncharacterized protein (LMOf2365_1472) from Listeria monocytogenes serotype 4b

PDB DOI: https://doi.org/10.2210/pdb3GNL/pdb

Classification: structural genomics, unknown function
Organism(s): Listeria monocytogenes serotype 4b str. F2365
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-03-17 Released: 2009-04-21
Deposition Author(s): Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.224 (Depositor), 0.220 (DCC)
R-Value Work:
0.196 (Depositor), 0.190 (DCC)
R-Value Observed:
0.198 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structure of uncharacterized protein (LMOf2365_1472) from Listeria monocytogenes serotype 4b

Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 55.23 kDa
Atom Count: 4,200
Modeled Residue Count: 464
Deposited Residue Count: 488
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein, DUF633, LMOf2365_1472	A, B	244	Listeria monocytogenes serotype 4b str. F2365	Mutation(s): 0 Gene Names: LMOf2365_1472
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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: 1.50 Å
R-Value Free: 0.224 (Depositor), 0.220 (DCC)
R-Value Work: 0.196 (Depositor), 0.190 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.273	α = 90
b = 84.802	β = 90
c = 91.168	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SHELXD	phasing
SHELXE	model building
CCP4	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-04-21

Deposition Author(s):

Ramagopal, U.A.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2009-04-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-11-27
Changes: Data collection, Database references, Structure summary

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.