6UM4

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
R-Value Work: 0.211
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

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
Modelled Residue Count: 3,908
Deposited Residue Count: 5,328
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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 M [auth D] SDF format, chain N [auth J] SDF format, chain O [auth J] SDF format, chain P [auth L] MOL2 format, chain M [auth D] MOL2 format, chain N [auth J] MOL2 format, chain O [auth J] MOL2 format, chain P [auth L]	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
R-Value Work: 0.211
R-Value Observed: 0.211
Space Group: P 1
Diffraction Data: https://doi.org/10.18430/m36um4

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

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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

Prepare Data

Validate Data

Deposit Data

Help and Resources

6UM4

Crystal structure of malate dehydrogenase from Naegleria fowleri ATCC 30863

Crystal structure of malate dehydrogenase from Naegleria fowleri ATCC 30863

Entity ID: 1

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)