PDB-4u04: Structure of a eukaryotic fic domain containing protein

ID or keywords:

Entry

Database: PDB / ID: 4u04

Title

Structure of a eukaryotic fic domain containing protein

Components

Adenosine monophosphate-protein transferase FICD

Keywords

TRANSFERASE / Adenylation / TPR / FIC

Function / homology

Function and homology information

protein deadenylylation / protein adenylylhydrolase activity / AMPylase activity / protein adenylylation / regulation of IRE1-mediated unfolded protein response / protein adenylyltransferase / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / negative regulation of GTPase activity / response to unfolded protein / Hsp70 protein binding ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.48 Å

Authors

Cole, A.R. / Bunney, T.D. / Katan, M.

Citation

Journal: Structure / Year: 2014
Title: Crystal structure of the human, FIC-domain containing protein HYPE and implications for its functions.
Authors: Bunney, T.D. / Cole, A.R. / Broncel, M. / Esposito, D. / Tate, E.W. / Katan, M.

History

Deposition	Jul 11, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Dec 10, 2014	Provider: repository / Type: Initial release
Revision 1.1	Feb 4, 2015	Group: Database references
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4u04.cif.gz	267.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4u04.ent.gz	218.1 KB	Display	PDB format
PDBx/mmJSON format	4u04.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4u04_validation.pdf.gz	464.2 KB	Display	wwPDB validaton report
Full document	4u04_full_validation.pdf.gz	471 KB	Display
Data in XML	4u04_validation.xml.gz	25.4 KB	Display
Data in CIF	4u04_validation.cif.gz	35.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u0/4u04 ftp://data.pdbj.org/pub/pdb/validation_reports/u0/4u04	HTTPS FTP

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Related structure data

Related structure data	4u07C 4u0sC 4u0uC 4u0zC 3cucS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6i7h-1 4u0z-7 4u0s-d 3rfu-4 6mno-d 4z7u-2 4u07-d 6mng-d 4ifc-d 4u0z-6 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#141 - Sep 2011 O-GlcNAc Transferase similarity (3) #198 - Jun 2016 Beta-galactosidase similarity (1) #166 - Oct 2013 Proteasome similarity (3) #230 - Feb 2019 Initiation Factor eIF4E similarity (3)

Deposited unit

A: Adenosine monophosphate-protein transferase FICD

B: Adenosine monophosphate-protein transferase FICD

hetero molecules

79.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	71.186, 76.809, 93.195
Angle α, β, γ (deg.)	90.00, 108.05, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Adenosine monophosphate-protein transferase FICD / HYPE / AMPylator FICD / FIC domain-containing protein / Huntingtin yeast partner E / Huntingtin- ...HYPE / AMPylator FICD / FIC domain-containing protein / Huntingtin yeast partner E / Huntingtin-interacting protein 13 / HIP-13 / Huntingtin-interacting protein E Mass: 39548.273 Da / Num. of mol.: 2 / Fragment: UNP residues 102-445 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FICD, HIP13, HYPE, UNQ3041/PRO9857 / Production host: Escherichia coli (E. coli) References: UniProt: Q9BVA6, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical	ChemComp-TAR / D(-)-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₆O₆
#3: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.06 Å³/Da / Density % sol: 59.84 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG 3350, 200mM Na K Tartrate, 100mM Bis-Tris Propane 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 29, 2012
Radiation	Monochromator: double xtal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9686 Å / Relative weight: 1
Reflection	Resolution: 2.48→47.193 Å / Num. all: 33248 / Num. obs: 33248 / % possible obs: 97.7 % / Redundancy: 3.1 % / B_iso Wilson estimate: 71.78 Å² / R_merge(I) obs: 0.088 / Net I/σ(I): 6.1
Reflection shell	Resolution: 2.48→2.61 Å / Redundancy: 3 % / R_merge(I) obs: 0.854 / % possible all: 97.7

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Processing

Software

Name	Version	Classification
BUSTER	2.10.0	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3cuc

3cuc

Resolution: 2.48→43.81 Å / Cor.coef. F_o:F_c: 0.9089 / Cor.coef. F_o:F_c free: 0.9001 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.332 / SU R_free Blow DPI: 0.234

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2448	1688	5.08 %	RANDOM
R_work	0.2179	-	-	-
obs	0.2193	33248	97.62 %	-

Displacement parameters

B_iso mean: 80.28 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.839 Å²	0 Å²	-22.3955 Å²
2-	-	4.6129 Å²	0 Å²
3-	-	-	-3.7739 Å²

Refine analyze

Luzzati coordinate error obs: 0.509 Å

Refinement step

Cycle: 1 / Resolution: 2.48→43.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9775	0	36	158	9969

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.009	9940	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	0.97	17898	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		2175	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		114	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		1531	HARMONIC	5
X-RAY DIFFRACTION	t_it		9940	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	2.5
X-RAY DIFFRACTION	t_other_torsion	18.53
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		699	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		10759	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.48→2.56 Å / Total num. of bins used: 17

	R_factor	Num. reflection	% reflection
R_free	0.3012	100	4.34 %
R_work	0.2573	2204	-
all	0.2591	2304	-
obs	-	-	97.62 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	-0.2623	0.692	0.7082	0.9223	-2.718	2.6683	0.0076	-0.0705	-0.033	0.0029	-0.0045	-0.0293	0.0324	0.0003	-0.0031	0.2587	0.088	0.0978	-0.1678	0.184	-0.0633	-38.6568	-9.0736	22.2322
2	2.644	-1.4298	-1.1981	2.919	1.329	0.8547	-0.0665	0.02	-0.046	0.084	0.0297	0.0663	0.1986	-0.1801	0.0368	0.1547	-0.0375	0.2612	-0.2081	0.0755	-0.0458	-43.1024	-4.989	10.2455
3	0.8853	-1.1527	-0.2802	1.0749	2.3914	1.9984	-0.0415	0.0596	0.0579	0.0598	0.0007	0.1237	-0.1421	0.0335	0.0408	0.003	0.0257	0.0672	-0.1896	0.0588	0.0724	-33.3533	8.1514	-0.665
4	4.1436	-1.7639	-0.095	3.1917	0.2097	4.026	-0.0983	-0.1779	0.1101	0.1102	-0.0356	-0.0587	0.0819	0.0397	0.134	-0.0369	0.1007	-0.168	-0.0812	-0.127	0.017	-2.842	-10.2938	-4.7924
5	5.2571	-1.5023	-1.9622	4.4828	2.2384	2.0316	-0.1594	0.2942	0.0994	-0.1017	0.1003	-0.1519	0.1758	0.2277	0.0591	-0.0164	-0.0736	0.0903	-0.1989	0.0028	-0.0919	-11.6897	-13.5345	-17.021
6	2.5943	-1.2313	-1.4524	7.0491	1.6265	3.6271	-0.3815	0.215	-0.1115	0.1251	0.1289	0.5998	0.2043	-0.1772	0.2526	-0.1573	-0.0054	-0.1049	-0.1422	0.0279	-0.1651	-24.913	-8.1418	-8.6615
7	0.4544	0.8584	-0.6594	0.9161	-0.467	0.0297	0.0001	0.0143	0.038	0.0441	-0.0078	-0.0319	-0.0107	0.1092	0.0077	0.0322	-0.1147	0.1392	0.0018	-0.0726	0.0451	37.5312	-35.8314	-46.6368
8	1.99	-0.2583	-3.3921	6.6415	1.9976	4.8016	-0.1082	0.1619	0.4031	0.1206	0.0897	0.0203	-0.0497	0.1034	0.0185	0.1551	-0.1504	0.3016	-0.301	0.0747	-0.1562	25.6846	-39.694	-51.4281
9	2.4668	-1.8259	-2.3846	5.2519	2.4507	-0.8346	0.0168	0.132	-0.0569	0.0687	-0.0264	0.0185	0.0867	-0.0259	0.0097	0.1622	0.0239	0.283	-0.304	-0.0119	-0.0981	14.7515	-52.4141	-41.439
10	0.6193	0.1594	-0.6468	0.146	-0.1969	0.0999	-0.0006	-0.0254	0.0154	0.0133	0.0016	0.0015	-0.0255	-0.0132	-0.001	0.0228	-0.0228	0.0462	-0.0213	-0.0103	0.0895	6.324	-52.209	-16.4367
11	2.6922	0.5166	-0.0309	4.4654	-2.6409	1.2433	-0.0442	-0.0491	-0.0454	0.1102	0.0486	-0.2487	0.143	0.0246	-0.0044	0.1579	0.152	0.1278	-0.2189	0.024	-0.1132	7.6073	-31.2171	-12.189
12	1.6881	-2.1263	-0.0308	2.4714	1.7806	2.9907	-0.1734	-0.1479	-0.0941	0.1198	0.0316	0.0187	0.2105	-0.1854	0.1418	0.1571	-0.0149	0.2723	-0.2477	0.0444	-0.0784	-4.436	-30.237	-22.4223
13	3.0248	-2.8488	-1.5312	5.6947	0.8195	3.824	-0.1479	0.1094	-0.0124	-0.3017	-0.0046	-0.1573	0.2999	-0.1824	0.1524	0.123	-0.06	0.2911	-0.304	-0.0118	-0.1596	5.4148	-35.7037	-34.2722

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{ A\|108 - A\|136 }
2	X-RAY DIFFRACTION	2	{ A\|137 - A\|177 }
3	X-RAY DIFFRACTION	3	{ A\|178 - A\|207 }
4	X-RAY DIFFRACTION	4	{ A\|222 - A\|255 }
5	X-RAY DIFFRACTION	5	{ A\|256 - A\|308 }
6	X-RAY DIFFRACTION	6	{ A\|309 - A\|433 }
7	X-RAY DIFFRACTION	7	{ B\|108 - B\|135 }
8	X-RAY DIFFRACTION	8	{ B\|136 - B\|179 }
9	X-RAY DIFFRACTION	9	{ B\|180 - B\|203 }
10	X-RAY DIFFRACTION	10	{ B\|204 - B\|222 }
11	X-RAY DIFFRACTION	11	{ B\|223 - B\|255 }
12	X-RAY DIFFRACTION	12	{ B\|256 - B\|308 }
13	X-RAY DIFFRACTION	13	{ B\|309 - B\|434 }

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