3I18 | pdb_00003i18

Crystal Structure of the PDZ domain of the SdrC-like protein (Lmo2051) from Listeria monocytogenes, Northeast Structural Genomics Consortium Target LmR166B

PDB DOI: https://doi.org/10.2210/pdb3I18/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Listeria monocytogenes
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-06-25 Released: 2009-07-14
Deposition Author(s): Forouhar, F., Lew, S., Seetharaman, J., Janjua, J., Xiao, R., Ciccosanti, C., Zhao, L., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.226 (Depositor), 0.275 (DCC)
R-Value Work:
0.193 (Depositor), 0.269 (DCC)
R-Value Observed:
0.194 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Northeast Structural Genomics Consortium Target LmR166B

Forouhar, F., Lew, S., Seetharaman, J., Janjua, J., Xiao, R., Ciccosanti, C., Zhao, L., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 11.28 kDa
Atom Count: 858
Modeled Residue Count: 95
Deposited Residue Count: 100
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lmo2051 protein	A	100	Listeria monocytogenes	Mutation(s): 0 Gene Names: lmo2051 EC: 3.4.21.53
UniProt
Find proteins for Q8Y5K8 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y5K8 Go to UniProtKB: Q8Y5K8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8Y5K8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BR Query on BR Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.226 (Depositor), 0.275 (DCC)
R-Value Work: 0.193 (Depositor), 0.269 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.705	α = 90
b = 90.475	β = 90
c = 51.811	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-07-14

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2009-07-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary