2IAF | pdb_00002iaf

Crystal structure of a fragment (residues 11 to 161) of L-serine dehydratase from Legionella pneumophila

PDB DOI: https://doi.org/10.2210/pdb2IAF/pdb

Classification: structural genomics, unknown function
Organism(s): Legionella pneumophila
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2006-09-07 Released: 2006-10-10
Deposition Author(s): Nocek, B., Mulligan, R., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.224 (Depositor), 0.232 (DCC)
R-Value Work:
0.195 (Depositor), 0.200 (DCC)
R-Value Observed:
0.196 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2IAF

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

Literature

Crystal structure of a fragment (residues 11 to 161) of L-serine dehydratase from Legionella pneumophila

Nocek, B., Mulligan, R., Moy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 16.79 kDa
Atom Count: 1,189
Modeled Residue Count: 140
Deposited Residue Count: 151
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein sdhL	A	151	Legionella pneumophila	Mutation(s): 4 Gene Names: sdhL EC: 4.3.1.17
UniProt
Find proteins for Q5WYB1 (Legionella pneumophila (strain Lens)) Explore Q5WYB1 Go to UniProtKB: Q5WYB1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5WYB1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		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: 2.05 Å
R-Value Free: 0.224 (Depositor), 0.232 (DCC)
R-Value Work: 0.195 (Depositor), 0.200 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.319	α = 90
b = 76.835	β = 90
c = 108.135	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-10-10

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2006-10-10
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.