6XR5 | pdb_00006xr5

Crystal Structure of Diphosphomevalonate decarboxylase (MVD1) Cryptococcus neoformans var. grubii serotype A

PDB DOI: https://doi.org/10.2210/pdb6XR5/pdb

Classification: LYASE
Organism(s): Cryptococcus neoformans H99
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-07-11 Released: 2020-09-23
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.182 (Depositor), 0.180 (DCC)
R-Value Work:
0.156 (Depositor), 0.150 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Diphosphomevalonate decarboxylase (MVD1) from Cryptococcus neoformans var. grubii serotype A

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

To be published.

Macromolecule Content

Total Structure Weight: 353.22 kDa
Atom Count: 28,006
Modeled Residue Count: 3,120
Deposited Residue Count: 3,224
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diphosphomevalonate decarboxylase	A, B, C, D, E A, B, C, D, E, F, G, H	403	Cryptococcus neoformans H99	Mutation(s): 0 Gene Names: CNAG_05125 EC: 4.1.1.33
UniProt
Find proteins for J9VRT5 (Cryptococcus neoformans (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487)) Explore J9VRT5 Go to UniProtKB: J9VRT5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	J9VRT5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADE Query on ADE Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain R [auth D] SDF format, chain T [auth E] SDF format, chain AA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth D] MOL2 format, chain T [auth E] MOL2 format, chain AA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain R [auth D] mmCIF format, chain T [auth E] mmCIF format, chain AA [auth H]	AA [auth H], K [auth A], N [auth B], R [auth D], T [auth E]	ADENINE C₅ H₅ N₅ GFFGJBXGBJISGV-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain R [auth D] Focus chain T [auth E] Interactions & Density Focus chain AA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain R [auth D] Focus chain T [auth E]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain Z [auth H] SDF format, chain Y [auth H] SDF format, chain V [auth F] SDF format, chain U [auth E] SDF format, chain S [auth E] SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain O [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain Z [auth H] MOL2 format, chain Y [auth H] MOL2 format, chain V [auth F] MOL2 format, chain U [auth E] MOL2 format, chain S [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain O [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain Z [auth H] mmCIF format, chain Y [auth H] mmCIF format, chain V [auth F] mmCIF format, chain U [auth E] mmCIF format, chain S [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain O [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A] J [auth A] L [auth B] M [auth B] O [auth C] I [auth A], J [auth A], L [auth B], M [auth B], O [auth C], P [auth D], Q [auth D], S [auth E], U [auth E], V [auth F], Y [auth H], Z [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth E] Focus chain V [auth F] Focus chain Y [auth H] Focus chain Z [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth E] Focus chain V [auth F] Focus chain Y [auth H] Focus chain Z [auth H]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain W [auth F] SDF format, chain X [auth G] MOL2 format, chain W [auth F] MOL2 format, chain X [auth G] mmCIF format, chain W [auth F] mmCIF format, chain X [auth G]	W [auth F], X [auth G]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain W [auth F] Focus chain X [auth G] Interactions & Density Focus chain W [auth F] Focus chain X [auth G]