5DIC | pdb_00005dic

Fatty acid binding protein OBP56a from the oral disk of the blowfly Phormia regina

PDB DOI: https://doi.org/10.2210/pdb5DIC/pdb

Classification: Odorant-binding protein
Organism(s): Phormia regina
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-08-31 Released: 2016-10-05
Deposition Author(s): Ishida, Y., Leal, W.S., Wilson, D.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.19 Å
R-Value Free:
0.168 (Depositor), 0.171 (DCC)
R-Value Work:
0.131 (Depositor), 0.135 (DCC)
R-Value Observed:
0.133 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

In preparation

Ishida, Y., Leal, W.S., Wilson, D.K.

To be published.

Macromolecule Content

Total Structure Weight: 13.79 kDa
Atom Count: 1,082
Modeled Residue Count: 115
Deposited Residue Count: 117
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Odorant-binding protein	A	117	Phormia regina	Mutation(s): 0 Gene Names: PregOBP56a
UniProt
Find proteins for L8B8J6 (Phormia regina) Explore L8B8J6 Go to UniProtKB: L8B8J6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	L8B8J6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLM Query on PLM Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.19 Å
R-Value Free: 0.168 (Depositor), 0.171 (DCC)
R-Value Work: 0.131 (Depositor), 0.135 (DCC)
R-Value Observed: 0.133 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.845	α = 105.35
b = 33.8	β = 106.44
c = 35.399	γ = 113.12

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-10-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-10-05
Type: Initial release
Version 1.1: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.