6UM4 | pdb_00006um4

Crystal structure of malate dehydrogenase from Naegleria fowleri ATCC 30863

PDB DOI: https://doi.org/10.2210/pdb6UM4/pdb

Classification: OXIDOREDUCTASE
Organism(s): Naegleria fowleri
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2019-10-09 Released: 2019-10-23
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.232 (Depositor), 0.235 (DCC)
R-Value Work:
0.211 (Depositor), 0.211 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6UM4

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of malate dehydrogenase from Naegleria fowleri ATCC 30863

Abendroth, J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 587.41 kDa
Atom Count: 31,359
Modeled Residue Count: 3,908
Deposited Residue Count: 5,328
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	444	Naegleria fowleri	Mutation(s): 0 Gene Names: mRNA1_NF0021050 EC: 1.1.1.37
UniProt
Find proteins for A0A5S8WFA9 (Naegleria fowleri) Explore A0A5S8WFA9 Go to UniProtKB: A0A5S8WFA9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A5S8WFA9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain P [auth L] SDF format, chain O [auth J] SDF format, chain N [auth J] SDF format, chain M [auth D] MOL2 format, chain P [auth L] MOL2 format, chain O [auth J] MOL2 format, chain N [auth J] MOL2 format, chain M [auth D] mmCIF format, chain P [auth L] mmCIF format, chain O [auth J] mmCIF format, chain N [auth J] mmCIF format, chain M [auth D]	M [auth D], N [auth J], O [auth J], P [auth L]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain M [auth D] Focus chain N [auth J] Focus chain O [auth J] Focus chain P [auth L] Interactions & Density Focus chain M [auth D] Focus chain N [auth J] Focus chain O [auth J] Focus chain P [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.232 (Depositor), 0.235 (DCC)
R-Value Work: 0.211 (Depositor), 0.211 (DCC)
R-Value Observed: 0.211 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.33	α = 91.093
b = 137.48	β = 89.998
c = 139.28	γ = 91.482

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
MoRDa	phasing
ARP/wARP	model building
BUCCANEER	model building

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-10-23

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2019-10-23
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-04-03
Changes: Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.