6VDH | pdb_00006vdh

Crystal structure of ancestral apicomplexan lactate dehydrogenase in alternate dimer configuration with sulfate.

PDB DOI: https://doi.org/10.2210/pdb6VDH/pdb

Classification: OXIDOREDUCTASE
Organism(s): Apicomplexa sp.
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2019-12-27 Released: 2020-01-29
Deposition Author(s): Theobald, D.L., Wirth, J.D., Classen, S., Perlmutter, N.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.236 (Depositor), 0.239 (DCC)
R-Value Work:
0.209 (Depositor), 0.211 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Mechanism of Bifunctionality in an Ancestral Apicomplexan Malate/Lactate Dehydrogenase

Theobald, D.L., Wirth, J.D., Classen, S., Perlmutter, N.

To be published.

Macromolecule Content

Total Structure Weight: 72 kDa
Atom Count: 5,065
Modeled Residue Count: 621
Deposited Residue Count: 660
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
lactate dehydrogenase	A, B	330	Apicomplexa sp.	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		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: 1.85 Å
R-Value Free: 0.236 (Depositor), 0.239 (DCC)
R-Value Work: 0.209 (Depositor), 0.211 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.38	α = 90
b = 105.44	β = 90
c = 151.45	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-01-29

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM096053

Revision History (Full details and data files)

Version 1.0: 2020-01-29
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, 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.