2IQX | pdb_00002iqx

Rat Phosphatidylethanolamine-Binding Protein Containing the S153E Mutation in the Complex with o-Phosphorylethanolamine

PDB DOI: https://doi.org/10.2210/pdb2IQX/pdb

Classification: HYDROLASE INHIBITOR
Organism(s): Rattus norvegicus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2006-10-14 Released: 2007-09-25
Deposition Author(s): Kim, Y., Joachimiak, G., Clark, M.C., Rosner, M., Joachimiak, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.261 (Depositor), 0.253 (DCC)
R-Value Work:
0.182 (Depositor), 0.177 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

Rat Phosphatidylethanolamine-Binding Crystal structure of Protein Containing the S153E Mutation in the Complex with o-Phosphorylethanolamine

Kim, Y., Joachimiak, G., Clark, M.C., Rosner, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 63.03 kDa
Atom Count: 4,964
Modeled Residue Count: 556
Deposited Residue Count: 561
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylethanolamine-binding protein 1	A, B, C	187	Rattus norvegicus	Mutation(s): 1
UniProt
Find proteins for P31044 (Rattus norvegicus) Explore P31044 Go to UniProtKB: P31044
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31044
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OPE Query on OPE Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth C] SDF format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth B]	D [auth A], E [auth B], F [auth C]	PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER C₂ H₈ N O₄ P SUHOOTKUPISOBE-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.261 (Depositor), 0.253 (DCC)
R-Value Work: 0.182 (Depositor), 0.177 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.971	α = 90
b = 57.211	β = 109.69
c = 80.886	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
EPMR	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-09-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-09-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-10-20
Changes: Database references
Version 1.3: 2023-08-30
Changes: Data collection, Refinement description

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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.