2A03 | pdb_00002a03

Superoxide dismutase protein from plasmodium berghei

PDB DOI: https://doi.org/10.2210/pdb2A03/pdb

Classification: OXIDOREDUCTASE
Organism(s): Plasmodium berghei
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-06-15 Released: 2005-06-21
Deposition Author(s): Holmes, M.A., Merritt, E.A., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free:
0.202 (Depositor), 0.210 (DCC)
R-Value Work:
0.171 (Depositor), 0.179 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Hypothetical protein from plasmodium berghei

Holmes, M.A., Merritt, E.A., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

To be published.

Macromolecule Content

Total Structure Weight: 47.43 kDa
Atom Count: 3,421
Modeled Residue Count: 394
Deposited Residue Count: 412
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fe-superoxide dismutase homolog	A, B	206	Plasmodium berghei	Mutation(s): 0 Gene Names: PB000490.02.0 EC: 1.15.1.1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free: 0.202 (Depositor), 0.210 (DCC)
R-Value Work: 0.171 (Depositor), 0.179 (DCC)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.111	α = 90
b = 105.111	β = 90
c = 207.935	γ = 120

Software Package:

Software Name	Purpose
EPMR	phasing
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-06-21

Deposition Author(s):

Holmes, M.A.

Merritt, E.A.

Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History (Full details and data files)

Version 1.0: 2005-06-21
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description