3FVB | pdb_00003fvb

Crystal structure of ferritin (bacterioferritin) from Brucella melitensis

PDB DOI: https://doi.org/10.2210/pdb3FVB/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Brucella abortus 2308
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-01-15 Released: 2009-02-03
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free:
0.215 (Depositor), 0.215 (DCC)
R-Value Work:
0.181 (Depositor), 0.181 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of ferritin from Brucella melitensis

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 42.96 kDa
Atom Count: 3,024
Modeled Residue Count: 322
Deposited Residue Count: 364
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacterioferritin	A, B	182	Brucella abortus 2308	Mutation(s): 0 Gene Names: bfr, BAB2_0675 EC: 1.16.3.1
UniProt
Find proteins for Q2YKI4 (Brucella abortus (strain 2308)) Explore Q2YKI4 Go to UniProtKB: Q2YKI4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2YKI4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM 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]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain R [auth B] MOL2 format, chain L [auth A] MOL2 format, chain R [auth B] mmCIF format, chain L [auth A] mmCIF format, chain R [auth B]	L [auth A], R [auth B]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain L [auth A] Focus chain R [auth B] Interactions & Density Focus chain L [auth A] Focus chain R [auth B]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain M [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain M [auth B]	D [auth A], E [auth A], M [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain M [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain Q [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B]	J [auth A], K [auth A], Q [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	F [auth A] G [auth A] H [auth A] N [auth B] O [auth B] F [auth A], G [auth A], H [auth A], N [auth B], O [auth B], P [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free: 0.215 (Depositor), 0.215 (DCC)
R-Value Work: 0.181 (Depositor), 0.181 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.81	α = 90
b = 174.81	β = 90
c = 174.81	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-02-03

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2009-02-03
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description