4GYT | pdb_00004gyt

Crystal structure of lpg0076 protein from Legionella pneumophila

PDB DOI: https://doi.org/10.2210/pdb4GYT/pdb

Classification: Structural Genomics, Unknown Function
Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-09-05 Released: 2012-09-26
Deposition Author(s): Michalska, K., Xu, X., Cui, H., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.213 (Depositor), 0.222 (DCC)
R-Value Work:
0.169 (Depositor), 0.179 (DCC)
R-Value Observed:
0.171 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4GYT

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of lpg0076 protein from Legionella pneumophila

Michalska, K., Xu, X., Cui, H., Savchenko, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 43.71 kDa
Atom Count: 2,988
Modeled Residue Count: 354
Deposited Residue Count: 388
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein	A, B	194	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 0 Gene Names: lpg0076
UniProt
Find proteins for Q5ZZD5 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZZD5 Go to UniProtKB: Q5ZZD5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5ZZD5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.213 (Depositor), 0.222 (DCC)
R-Value Work: 0.169 (Depositor), 0.179 (DCC)
R-Value Observed: 0.171 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.847	α = 90
b = 85.872	β = 90
c = 103.845	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELX	model building
MLPHARE	phasing
DM	model building
BUCCANEER	model building
ARP/wARP	model building
Coot	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
DM	phasing
BUCCANEER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-09-26

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2012-09-26
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.