8ARU | pdb_00008aru

Crystal Structure of human formylglycine generating enzyme

PDB DOI: https://doi.org/10.2210/pdb8ARU/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2022-08-17 Released: 2023-08-23
Deposition Author(s): Neumann, P., Dickmanns, A., Ficner, R., Rudolph, M.G.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.08 Å
R-Value Free:
0.174 (Depositor), 0.178 (DCC)
R-Value Work:
0.140 (Depositor), 0.145 (DCC)
R-Value Observed:
0.142 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of human formylglycine generating enzyme E130A mutant

Kowal, J., Neumann, P., Dickmanns, A., Ficner, R., Schlotawa, L., Niemann, H., Schlotawa, L., Rudolph, M.G.

To be published.

Macromolecule Content

Total Structure Weight: 36.58 kDa
Atom Count: 2,763
Modeled Residue Count: 278
Deposited Residue Count: 323
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formylglycine-generating enzyme	A	323	Homo sapiens	Mutation(s): 0 Gene Names: SUMF1, PSEC0152, UNQ3037/PRO9852 EC: 1.8.3.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NBK3 (Homo sapiens) Explore Q8NBK3 Go to UniProtKB: Q8NBK3
PHAROS: Q8NBK3 GTEx: ENSG00000144455
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NBK3
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A	Go to GlyGen: Q8NBK3-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.08 Å
R-Value Free: 0.174 (Depositor), 0.178 (DCC)
R-Value Work: 0.140 (Depositor), 0.145 (DCC)
R-Value Observed: 0.142 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.497	α = 90
b = 61.562	β = 90
c = 109.33	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-08-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-08-23
Type: Initial release
Version 1.1: 2024-11-20
Changes: Structure summary
Version 1.2: 2026-03-04
Changes: 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.