PDB-5xwm: human ERp44 zinc-bound form

ID or keywords:

Entry

Database: PDB / ID: 5xwm

Title

human ERp44 zinc-bound form

Components

Endoplasmic reticulum resident protein 44

Keywords

OXIDOREDUCTASE /

chaperone

Function / homology

Function and homology information

glycoprotein metabolic process /

protein disulfide isomerase activity / response to unfolded protein /

endoplasmic reticulum-Golgi intermediate compartment / response to endoplasmic reticulum stress / cell redox homeostasis / specific granule lumen /

protein folding /

endoplasmic reticulum lumen / Neutrophil degranulation ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.45 Å

Authors

Watanabe, S. / Harayama, M. / Inaba, K.

Citation

Journal: Nat Commun / Year: 2019
Title: Zinc regulates ERp44-dependent protein quality control in the early secretory pathway.
Authors: Watanabe, S. / Amagai, Y. / Sannino, S. / Tempio, T. / Anelli, T. / Harayama, M. / Masui, S. / Sorrentino, I. / Yamada, M. / Sitia, R. / Inaba, K.

History

Deposition	Jun 30, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 2, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jul 17, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Mar 27, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5xwm.cif.gz	596.2 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xw/5xwm ftp://data.pdbj.org/pub/pdb/validation_reports/xw/5xwm	HTTPS FTP

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Related structure data

Similar structure data	2nqu-d 2nqs-d 1g8l-d 1g8r-d 2nro-d 2nqr-d 2nqq-2 6asl-1 2nqv-d 2nqk-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#32 - Aug 2002 Chaperones similarity (1) #108 - Dec 2008 Hsp90 similarity (1) #110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (1) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1)

Deposited unit

A: Endoplasmic reticulum resident protein 44

B: Endoplasmic reticulum resident protein 44

C: Endoplasmic reticulum resident protein 44

D: Endoplasmic reticulum resident protein 44

hetero molecules

178 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Endoplasmic reticulum resident protein 44

C: Endoplasmic reticulum resident protein 44

hetero molecules

defined by author&software
Evidence: gel filtration, Dimer
89.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Endoplasmic reticulum resident protein 44

D: Endoplasmic reticulum resident protein 44

hetero molecules

defined by author&software
89.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	175.150, 175.150, 407.810
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	178
Space group name H-M	P6₁22

#1: Protein	Endoplasmic reticulum resident protein 44 / ERp44 / Thioredoxin domain-containing protein 4 Mass: 44345.746 Da / Num. of mol.: 4 / Fragment: UNP residues 39-406 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ERP44, KIAA0573, TXNDC4, UNQ532/PRO1075 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BS26
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 527 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 5.09 Å³/Da / Density % sol: 75.84 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: Na malonate or Tascimate

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1
3	100	1
4	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	SPring-8	BL44XU	1	0.9
SYNCHROTRON	SPring-8	BL44XU	2	0.9
SYNCHROTRON	Photon Factory	BL-1A	3	1.1
SYNCHROTRON	Photon Factory	BL-1A	4	1.1

Detector

Type	ID	Detector	Date
RAYONIX MX300HE	1	CCD	Oct 6, 2015
RAYONIX MX300HE	2	CCD	Apr 20, 2016
DECTRIS EIGER X 4M	3	PIXEL	Dec 17, 2015
DECTRIS EIGER X 4M	4	PIXEL	Mar 7, 2016

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	2
3	SINGLE WAVELENGTH	M	x-ray	3
4	SINGLE WAVELENGTH	M	x-ray	4

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9	1
2	1.1	1
3		1
4		1

Reflection

Resolution: 2.45→50 Å / Num. obs: 135470 / % possible obs: 100 % / Redundancy: 64.7 % / CC_1/2: 1 / R_merge(I) obs: 0.156 / Net I/σ(I): 33.1

Reflection shell

Resolution: 2.45→2.51 Å / Redundancy: 59.2 % / R_merge(I) obs: 1.09 / Mean I/σ(I) obs: 5.15 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XDS		data processing
XSCALE		data scaling
SHELXDE		phasing
XDS		data reduction

Refinement

Method to determine structure:

SAD / Resolution: 2.45→44.056 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 19.98

	R_factor	Num. reflection	% reflection
R_free	0.2137	6621	4.89 %
R_work	0.1823	-	-
obs	0.1838	135458	99.99 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.45→44.056 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11396	0	18	527	11941

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	11712
X-RAY DIFFRACTION	f_angle_d	0.927	15822
X-RAY DIFFRACTION	f_dihedral_angle_d	15.86	7042
X-RAY DIFFRACTION	f_chiral_restr	0.057	1699
X-RAY DIFFRACTION	f_plane_restr	0.005	2103

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.45-2.4778	0.3366	199	0.3074	4249	X-RAY DIFFRACTION	100
2.4778-2.507	0.3147	225	0.2938	4240	X-RAY DIFFRACTION	100
2.507-2.5376	0.3194	210	0.2912	4229	X-RAY DIFFRACTION	100
2.5376-2.5697	0.3227	203	0.2884	4228	X-RAY DIFFRACTION	100
2.5697-2.6035	0.3323	233	0.2749	4199	X-RAY DIFFRACTION	100
2.6035-2.6392	0.2947	208	0.2717	4250	X-RAY DIFFRACTION	100
2.6392-2.6769	0.2942	205	0.2665	4253	X-RAY DIFFRACTION	100
2.6769-2.7168	0.3051	228	0.2605	4207	X-RAY DIFFRACTION	100
2.7168-2.7593	0.28	220	0.2504	4273	X-RAY DIFFRACTION	100
2.7593-2.8045	0.288	234	0.2436	4210	X-RAY DIFFRACTION	100
2.8045-2.8528	0.276	220	0.238	4220	X-RAY DIFFRACTION	100
2.8528-2.9047	0.2519	231	0.238	4268	X-RAY DIFFRACTION	100
2.9047-2.9606	0.2879	217	0.2485	4241	X-RAY DIFFRACTION	100
2.9606-3.021	0.2911	234	0.2402	4263	X-RAY DIFFRACTION	100
3.021-3.0866	0.2545	230	0.2225	4223	X-RAY DIFFRACTION	100
3.0866-3.1584	0.2555	197	0.206	4288	X-RAY DIFFRACTION	100
3.1584-3.2374	0.2199	199	0.1953	4303	X-RAY DIFFRACTION	100
3.2374-3.3249	0.2308	228	0.1847	4246	X-RAY DIFFRACTION	100
3.3249-3.4227	0.2131	241	0.1845	4249	X-RAY DIFFRACTION	100
3.4227-3.5331	0.2218	229	0.1802	4283	X-RAY DIFFRACTION	100
3.5331-3.6593	0.1866	245	0.1639	4277	X-RAY DIFFRACTION	100
3.6593-3.8058	0.1918	232	0.1477	4289	X-RAY DIFFRACTION	100
3.8058-3.9789	0.1832	216	0.1443	4305	X-RAY DIFFRACTION	100
3.9789-4.1885	0.1568	230	0.1312	4307	X-RAY DIFFRACTION	100
4.1885-4.4507	0.1597	240	0.1277	4313	X-RAY DIFFRACTION	100
4.4507-4.7939	0.1276	221	0.1151	4353	X-RAY DIFFRACTION	100
4.7939-5.2757	0.1595	193	0.1232	4420	X-RAY DIFFRACTION	100
5.2757-6.0374	0.1609	185	0.1395	4456	X-RAY DIFFRACTION	100
6.0374-7.6001	0.1929	226	0.1712	4478	X-RAY DIFFRACTION	100
7.6001-44.0632	0.1972	242	0.174	4717	X-RAY DIFFRACTION	100

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	1.461	-0.7571	-0.1876	4.8821	-0.8613	1.6503	-0.3593	-0.2711	0.198	0.0484	0.5759	-0.1854	0.3097	-0.0716	-0.1834	0.4787	0.1796	0.0023	0.5878	0.0105	0.3603	2.1238	19.4759	48.3155
2	2.8959	-0.0317	-0.5972	0.8189	-0.1901	1.0861	0.0335	0.5415	-0.2789	-0.2948	-0.0358	-0.0752	0.0663	-0.1581	-0.011	0.3558	0.0135	0.076	0.3814	-0.1487	0.3317	-13.3275	65.0166	4.1632
3	1.1005	-0.2337	-0.2323	3.4486	0.2062	0.792	-0.1421	-0.3206	-0.0989	0.4217	0.19	-0.637	0.1165	0.2108	-0.0229	0.2564	0.0624	-0.0494	0.3947	-0.0716	0.4008	-5.9834	63.4721	43.5084
4	2.5409	-0.2864	-1.1795	0.7709	0.3635	1.0956	-0.0466	0.1872	-0.0547	0.2144	-0.059	0.1657	0.1622	-0.2574	0.0643	0.3476	-0.0088	0.0641	0.3323	-0.0543	0.2634	27.3467	64.3847	-11.459

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain 'A' and resid 1 through 358)
2	X-RAY DIFFRACTION	2	(chain 'B' and resid 1 through 365)
3	X-RAY DIFFRACTION	3	(chain 'C' and resid 2 through 358)
4	X-RAY DIFFRACTION	4	(chain 'D' and resid 0 through 377)

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