4N4X | pdb_00004n4x

Crystal Structure of the MBP fused human SPLUNC1 (native form)

PDB DOI: https://doi.org/10.2210/pdb4N4X/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Escherichia coli, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-10-08 Released: 2014-09-17
Deposition Author(s): Ning, F., Wang, C., Niu, L., Chu, H.W., Zhang, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.268 (Depositor), 0.258 (DCC)
R-Value Work:
0.215 (Depositor), 0.207 (DCC)
R-Value Observed:
0.216 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4N4X

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

Literature

Lipid ligands of human SPLUNC1

Ning, F., Wang, C., Niu, L., Chu, H.W., Zhang, G.

To be published.

Macromolecule Content

Total Structure Weight: 62.88 kDa
Atom Count: 4,140
Modeled Residue Count: 535
Deposited Residue Count: 584
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic/Palate lung and nasal epithelium clone fusion protein	A	584	Escherichia coli, Homo sapiens This entity is chimeric	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9 Go to UniProtKB: P0AEX9
Find proteins for Q9NP55 (Homo sapiens) Explore Q9NP55 Go to UniProtKB: Q9NP55
PHAROS: Q9NP55 GTEx: ENSG00000198183
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	Q9NP55 P0AEX9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG 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]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.268 (Depositor), 0.258 (DCC)
R-Value Work: 0.215 (Depositor), 0.207 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.087	α = 90
b = 119.087	β = 90
c = 98.541	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-09-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-09-17
Type: Initial release
Version 1.1: 2015-11-11
Changes: Source and taxonomy
Version 1.2: 2017-08-02
Changes: Advisory, Refinement description, Source and taxonomy
Version 1.3: 2019-07-17
Changes: Data collection, Refinement description
Version 1.4: 2024-11-06
Changes: Advisory, 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.