6EBT | pdb_00006ebt

Crystal structure of recombinant mutant N107T of human fumarase

PDB DOI: https://doi.org/10.2210/pdb6EBT/pdb

Classification: LYASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2018-08-07 Released: 2019-08-21
Deposition Author(s): Ajalla, M.A.A., Nonato, M.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.185 (Depositor), 0.188 (DCC)
R-Value Work:
0.150 (Depositor), 0.152 (DCC)
R-Value Observed:
0.152 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of recombinant mutant N107T of human fumarase

Ajalla, M.A.A., Nonato, M.C.

To be published.

Macromolecule Content

Total Structure Weight: 100.71 kDa
Atom Count: 7,445
Modeled Residue Count: 924
Deposited Residue Count: 932
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fumarate hydratase, mitochondrial	A, B	466	Homo sapiens	Mutation(s): 1 Gene Names: FH EC: 4.2.1.2
UniProt & NIH Common Fund Data Resources
Find proteins for P07954 (Homo sapiens) Explore P07954 Go to UniProtKB: P07954
PHAROS: P07954 GTEx: ENSG00000091483
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07954
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.185 (Depositor), 0.188 (DCC)
R-Value Work: 0.150 (Depositor), 0.152 (DCC)
R-Value Observed: 0.152 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 188.816	α = 90
b = 188.816	β = 90
c = 114.145	γ = 120

Software Package:

Software Name	Purpose
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-08-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-08-21
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.