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), 0.182 (DCC)
R-Value Work:
0.156 (Depositor), 0.157 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6XR5

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

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 T [auth E] SDF format, chain R [auth D] SDF format, chain N [auth B] SDF format, chain K [auth A] SDF format, chain AA [auth H] MOL2 format, chain T [auth E] MOL2 format, chain R [auth D] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain AA [auth H] mmCIF format, chain T [auth E] mmCIF format, chain R [auth D] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A] 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 X [auth G] SDF format, chain W [auth F] MOL2 format, chain X [auth G] MOL2 format, chain W [auth F] mmCIF format, chain X [auth G] mmCIF format, chain W [auth F]	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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.182 (Depositor), 0.182 (DCC)
R-Value Work: 0.156 (Depositor), 0.157 (DCC)
R-Value Observed: 0.156 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.51	α = 90
b = 168.05	β = 90.14
c = 101.21	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
MoRDa	phasing
Coot	model building

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-09-23

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2020-09-23
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, 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.