7DLB | pdb_00007dlb

Crassostrea gigas ferritin mutant-D119K

PDB DOI: https://doi.org/10.2210/pdb7DLB/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Magallana gigas
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-11-26 Released: 2021-12-01
Deposition Author(s): Li, H., Zang, J., Wang, Z., Du, M.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.240 (Depositor), 0.240 (DCC)
R-Value Work:
0.195 (Depositor), 0.196 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crassostrea gigas ferritin mutant-D119K

Li, H., Zang, J., Wang, Z., Du, M.

To be published.

Macromolecule Content

Total Structure Weight: 40.13 kDa
Atom Count: 2,899
Modeled Residue Count: 338
Deposited Residue Count: 342
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin	A, B	171	Magallana gigas	Mutation(s): 1 Gene Names: fer, CGI_10027591 EC: 1.16.3.1
UniProt
Find proteins for Q70MM3 (Magallana gigas) Explore Q70MM3 Go to UniProtKB: Q70MM3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q70MM3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		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: 2.50 Å
R-Value Free: 0.240 (Depositor), 0.240 (DCC)
R-Value Work: 0.195 (Depositor), 0.196 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.702	α = 90
b = 150.702	β = 90
c = 150.702	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SHELXD	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-12-01

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31730069

Revision History (Full details and data files)

Version 1.0: 2021-12-01
Type: Initial release
Version 1.1: 2023-11-29
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.