3B6Y | pdb_00003b6y

Crystal Structure of the Second HIN-200 Domain of Interferon-Inducible Protein 16

PDB DOI: https://doi.org/10.2210/pdb3B6Y/pdb

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

Deposited: 2007-10-29 Released: 2007-11-13
Deposition Author(s): Liao, J.C.C., Lam, R., Ravichandran, M., Duan, S., Tempel, W., Chirgadze, N.Y., Arrowsmith, C.H., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.292 (Depositor), 0.291 (DCC)
R-Value Work:
0.226 (Depositor), 0.227 (DCC)
R-Value Observed:
0.229 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure Analysis of the Second HIN Domain of IFI16.

Liao, J.C.C., Lam, R., Ravichandran, M., Duan, S., Tempel, W., Chirgadze, N.Y., Arrowsmith, C.H.

To be published.

Macromolecule Content

Total Structure Weight: 45.49 kDa
Atom Count: 2,965
Modeled Residue Count: 369
Deposited Residue Count: 400
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-interferon-inducible protein Ifi-16	A, B	200	Homo sapiens	Mutation(s): 0 Gene Names: IFI16, IFNGIP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16666 (Homo sapiens) Explore Q16666 Go to UniProtKB: Q16666
PHAROS: Q16666 GTEx: ENSG00000163565
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q16666
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.292 (Depositor), 0.291 (DCC)
R-Value Work: 0.226 (Depositor), 0.227 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.999	α = 90
b = 92.887	β = 90
c = 100.372	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-11-13

Deposition Author(s):

Ravichandran, M.

Chirgadze, N.Y.

Arrowsmith, C.H.

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2007-11-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-30
Changes: 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.