3WXQ

Serial femtosecond X-ray structure of human fatty acid-binding protein type-3 (FABP3) in complex with stearic acid (C18:0) determined using X-ray free-electron laser at SACLA

PDB DOI: https://doi.org/10.2210/pdb3WXQ/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-08-04 Released: 2014-11-05
Deposition Author(s): Mizohata, E., Suzuki, M., Kakinouchi, K., Sugiyama, S., Murata, M., Sugahara, M., Nango, E., Tanaka, T., Tanaka, R., Tono, K., Song, C., Hatsui, T., Joti, Y., Yabashi, M., Iwata, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.222
R-Value Work: 0.178
R-Value Observed: 0.180

wwPDB Validation 3D Report Full Report

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

Literature

Grease matrix as a versatile carrier of proteins for serial crystallography

Sugahara, M., Mizohata, E., Nango, E., Suzuki, M., Tanaka, T., Masuda, T., Tanaka, R., Shimamura, T., Tanaka, Y., Suno, C., Ihara, K., Pan, D., Kakinouchi, K., Sugiyama, S., Murata, M., Inoue, T., Tono, K., Song, C., Park, J., Kameshima, T., Hatsui, T., Joti, Y., Yabashi, M., Iwata, S.

(2015) Nat Methods 12: 61-63

PubMed: 25384243 Search on PubMed
DOI: https://doi.org/10.1038/nmeth.3172
Primary Citation of Related Structures:
3WUL, 3WUM, 3WXQ, 3WXS, 3WXT, 3WXU, 4W4Q

PubMed Abstract:
Serial femtosecond X-ray crystallography (SFX) has revolutionized atomic-resolution structural investigation by expanding applicability to micrometer-sized protein crystals, even at room temperature, and by enabling dynamics studies. However, reliable crystal-carrying media for SFX are lacking. Here we introduce a grease-matrix carrier for protein microcrystals and obtain the structures of lysozyme, glucose isomerase, thaumatin and fatty acid-binding protein type 3 under ambient conditions at a resolution of or finer than 2 Å.

Organizational Affiliation

RIKEN SPring-8 Center, Sayo, Japan.

Macromolecule Content

Total Structure Weight: 15.16 kDa
Atom Count: 1,230
Modelled Residue Count: 133
Deposited Residue Count: 133
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid-binding protein, heart	A	133	Homo sapiens	Mutation(s): 0 Gene Names: FABP3, FABP11, MDGI
UniProt & NIH Common Fund Data Resources
Find proteins for P05413 (Homo sapiens) Explore P05413 Go to UniProtKB: P05413
PHAROS: P05413 GTEx: ENSG00000121769
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05413
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
STE Query on STE Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	STEARIC ACID C₁₈ H₃₆ O₂ QIQXTHQIDYTFRH-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.222
R-Value Work: 0.178
R-Value Observed: 0.180
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.707	α = 90
b = 54.851	β = 90
c = 70.656	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
CrystFEL	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-11-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-11-05
Type: Initial release
Version 1.1: 2018-01-24
Changes: Data collection
Version 1.2: 2018-03-14
Changes: Data collection, Database references, Source and taxonomy
Version 1.3: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description