PDB-4nwy: Crystal structure of the b' domain of human protein disulfide iso...

ID or keywords:

Entry

Database: PDB / ID: 4nwy

Title

Crystal structure of the b' domain of human protein disulfide isomerase-like protein of the testis (PDILT)

Components

Protein disulfide-isomerase-like protein of the testis

Keywords

ISOMERASE / thioredoxin-like fold / substrate-binding domain / endoplasmic reticulum

Function / homology

Function and homology information

germ cell migration / protein disulfide isomerase activity / spermatid development / protein folding chaperone / protein folding / endoplasmic reticulum
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Bastos-Aristizabal, S. / Kozlov, G. / Gehring, K.

Citation

Journal: Sci Rep / Year: 2014
Title: Structure of the substrate-binding b' domain of the Protein disulfide isomerase-like protein of the testis.
Authors: Bastos-Aristizabal, S. / Kozlov, G. / Gehring, K.

History

Deposition	Dec 7, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 2, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4nwy.cif.gz	217.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4nwy.ent.gz	177.8 KB	Display	PDB format
PDBx/mmJSON format	4nwy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4nwy_validation.pdf.gz	458.5 KB	Display	wwPDB validaton report
Full document	4nwy_full_validation.pdf.gz	461.1 KB	Display
Data in XML	4nwy_validation.xml.gz	21.5 KB	Display
Data in CIF	4nwy_validation.cif.gz	30 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nw/4nwy ftp://data.pdbj.org/pub/pdb/validation_reports/nw/4nwy	HTTPS FTP

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Related structure data

Related structure data	3bj5S S: Starting model for refinement
Similar structure data	1fhs-d 4p9z-d 2gjh-d 6hyl-2 3ihx-1 2gbs-d 1i87-d 2djk-d 2d9x-d 1ak7-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) 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

Related structure data

3bj5S

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#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: Protein disulfide-isomerase-like protein of the testis

B: Protein disulfide-isomerase-like protein of the testis

C: Protein disulfide-isomerase-like protein of the testis

D: Protein disulfide-isomerase-like protein of the testis

hetero molecules

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

1

A: Protein disulfide-isomerase-like protein of the testis

hetero molecules

defined by author
15.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Protein disulfide-isomerase-like protein of the testis

hetero molecules

defined by author
15.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Protein disulfide-isomerase-like protein of the testis

hetero molecules

defined by author
15.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Protein disulfide-isomerase-like protein of the testis

defined by author
15.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	60.977, 119.736, 33.291
Angle α, β, γ (deg.)	90.00, 90.90, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Protein disulfide-isomerase-like protein of the testis Mass: 15545.648 Da / Num. of mol.: 4 / Fragment: b' domain (UNP residues 258-386) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDILT / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8N807, protein disulfide-isomerase
#2: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH₂O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 218 / 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: 1.95 Å³/Da / Density % sol: 37.06 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 0.2 M sodium formate, 0.1 M Bicine pH 9.0, 18% PEG3350, 0.1 M cobaltous chloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 7, 2007
Radiation	Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.977 Å / Relative weight: 1
Reflection	Resolution: 2→50 Å / Num. all: 30405 / Num. obs: 30080 / % possible obs: 98.93 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.2 % / R_merge(I) obs: 0.043 / Net I/σ(I): 24.7
Reflection shell	Resolution: 2→2.03 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.211 / Mean I/σ(I) obs: 4.2 / Num. unique all: 2079 / % possible all: 92.8

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3bj5

3bj5

Resolution: 2→50 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.909 / SU B: 7.96 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.232 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23828	1607	5.1 %	RANDOM
R_work	0.19518	-	-	-
obs	0.19739	30080	98.93 %	-
all	-	30405	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 24.697 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.38 Å²	0 Å²	0.04 Å²
2-	-	1.44 Å²	0 Å²
3-	-	-	-1.06 Å²

Refinement step

Cycle: LAST / Resolution: 2→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4030	0	12	218	4260

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	4182
X-RAY DIFFRACTION	r_angle_refined_deg	0.97	1.957	5633
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.277	5	503
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.387	24.03	201
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.616	15	788
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.229	15	23
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	621
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	3101
X-RAY DIFFRACTION	r_nbd_refined	0.18	0.2	1731
X-RAY DIFFRACTION	r_nbtor_refined	0.299	0.2	2849
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.119	0.2	215
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.18	0.2	128
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.156	0.2	27
X-RAY DIFFRACTION	r_mcbond_it	0.435	1.5	2578
X-RAY DIFFRACTION	r_mcangle_it	0.749	2	4038
X-RAY DIFFRACTION	r_scbond_it	0.98	3	1820
X-RAY DIFFRACTION	r_scangle_it	1.625	4.5	1587

LS refinement shell

Resolution: 2.004→2.056 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.232	99	-
R_work	0.188	2079	-
obs	-	-	92.8 %

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	2.2088	1.2985	1.0936	7.3737	-0.6705	6.3637	-0.1625	0.0112	0.2741	-0.1457	0.1346	-0.4428	-0.5053	0.3321	0.0279	0.0213	-0.0319	0.008	0.0042	-0.022	0.0335	-3.1652	11.2877	-2.255
2	1.1641	-0.0061	0.3782	1.6653	0.1487	2.6036	-0.0136	0.0433	-0.0237	-0.005	0.0623	-0.1819	0.0193	0.1942	-0.0487	0.0758	0.0041	-0.0012	0.0671	-0.0138	0.0589	-6.4035	-0.9978	-0.3082
3	0.8276	0.2014	-0.2786	2.432	0.9407	3.1575	0.0586	0.0072	0.1156	-0.0618	-0.0003	0.1586	-0.1743	-0.2467	-0.0583	0.0372	0.0281	0.0024	0.0626	0.0182	0.0296	-17.4473	4.957	1.5027
4	4.0159	1.4016	-0.8871	12.8222	-6.6061	11.6747	-0.0294	-0.0891	0.0869	0.144	0.0251	0.4309	-0.4033	-0.326	0.0044	-0.0179	0.0519	-0.0108	0.0353	-0.0158	-0.0074	-18.5951	2.0969	-7.6474
5	1.6882	-2.6363	2.5769	6.0322	-5.3357	6.1468	0.0643	0.0491	-0.193	-0.0637	0.1221	0.2519	0.0713	-0.0824	-0.1865	0.0559	-0.0057	0.0003	0.0596	-0.0293	0.0533	-12.5995	-4.1695	-12.8456
6	1.5899	6.7514	-1.8663	32.7324	-9.8033	3.059	-0.1866	-0.3065	0.5542	-0.503	0.4042	1.2398	0.0514	0.2342	-0.2176	0.0289	0.0177	0.0282	0.062	-0.0189	0.0338	-18.3934	18.3735	-24.4704
7	12.7557	-4.788	1.9553	18.8714	-6.4824	10.3838	0.0105	-0.1594	-0.7612	0.3888	0.2142	0.827	0.5627	-0.3717	-0.2247	0.0081	-0.066	0.0301	0.005	-0.0018	-0.004	-31.4235	-28.0449	-14.408
8	1.6881	-2.2609	8.6967	4.6625	-12.6772	45.4512	-0.2628	-0.5363	-0.4468	-0.4191	0.1114	0.0219	1.9233	-2.9828	0.1514	0.0973	-0.1547	-0.0261	0.1944	0.0377	0.0757	-32.7987	-33.8	-20.906
9	1.9331	-0.0973	-0.1593	1.3091	0.5284	4.8754	0.0192	0.0333	0.0747	0.0206	-0.042	0.0949	0.0223	-0.194	0.0229	0.0364	-0.0032	-0.0046	0.039	0.0068	0.0511	-28.4894	-16.6201	-16.8566
10	1.5128	-0.185	0.7958	1.5427	-0.7835	5.0019	0.0079	0.0165	-0.1365	-0.0125	0.0091	-0.0004	0.261	0.0272	-0.017	0.0543	0.0091	0.0064	0.0215	-0.0182	0.0418	-22.4692	-23.6307	-15.9942
11	4.8413	-2.2254	0.4669	5.3097	0.7867	2.766	0.0371	0.2057	-0.1413	0.0036	-0.044	-0.2327	0.3049	0.2684	0.0068	0.0473	0.0225	0.0154	0.0387	0.0182	-0.0272	-19.71	-18.1845	-24.2229
12	4.5481	-3.3875	-3.8384	9.6124	9.5317	13.1483	0.0361	0.1639	0.2117	-0.0479	0.1232	-0.6196	0.149	0.3487	-0.1592	0.0357	0.0017	-0.0168	0.0826	0.0339	0.0171	-19.5338	-19.7785	-33.2048
13	36.5947	11.2743	-0.5318	9.6549	-1.9526	10.8071	-0.2547	0.8568	0.4592	-0.5081	0.1957	0.3799	-0.0258	-0.5367	0.0589	-0.0512	-0.0251	-0.0319	0.0216	0.0504	0.0152	-16.2655	38.4771	-31.3905
14	24.7958	-12.281	2.4421	7.9221	1.605	4.5471	0.0143	1.3485	-1.5421	-0.5298	0.1802	0.9391	0.468	-0.4068	-0.1945	0.1504	-0.2381	0.0602	0.1397	-0.0459	0.0247	-13.7738	30.555	-36.3469
15	5.8199	1.2925	-1.4068	1.797	0.7039	2.8618	0.1072	0.0728	0.5265	0.1602	0.0443	0.0598	-0.1249	-0.0453	-0.1515	0.014	-0.0033	0.0123	0.0013	-0.0012	0.082	-7.9527	43.6559	-24.283
16	4.0173	-0.0727	-0.8488	3.3236	0.263	1.9325	0.0613	0.0262	-0.2743	0.1593	0.0011	-0.0387	0.0336	0.0049	-0.0623	0.0137	-0.0024	0.0061	-0.019	0.0031	0.0566	-9.0253	33.7436	-22.3009
17	6.1568	1.7866	0.9493	16.1712	2.0771	1.7521	-0.0199	0.1183	-0.6057	-0.4587	0.0715	-0.5391	0.038	0.3855	-0.0516	-0.0335	0.0056	0.0205	0.023	-0.0009	0.0876	4.347	35.9564	-25.0188
18	0.2947	0.7903	-0.4567	5.5261	-4.8831	4.6362	-0.0807	0.3344	0.0741	0.1005	-0.1728	-0.5941	-0.1951	-0.0676	0.2535	0.2272	0.0347	0.1477	-0.0665	0.0363	0.1902	-5.9465	20.0156	-9.7391
19	11.0827	-3.4217	-2.2963	5.4708	-0.2065	5.0906	0.1229	1.1168	1.0312	-0.8633	0.0358	-1.0962	-0.7118	0.4108	-0.1587	-0.0016	-0.1033	0.0804	0.085	0.0604	0.1708	-11.2752	68.5852	-50.0001
20	7.0112	0.2282	-0.0363	3.0433	0.3711	1.7826	-0.0374	-0.006	-0.4265	0.1687	0.0131	-0.3911	0.0721	-0.1516	0.0243	-0.0206	-0.0248	-0.0107	0.0233	-0.0185	0.0899	-17.0554	57.0513	-41.2217
21	9.6525	0.0744	2.0127	2.1451	0.0932	2.9965	0.0405	0.0087	0.4217	0.1485	-0.0168	-0.2076	-0.1082	0.0207	-0.0237	-0.032	-0.0067	-0.0105	-0.0559	-0.0239	0.0759	-13.952	65.7448	-38.7392
22	4.6462	0.8042	0.3059	6.5514	0.8024	4.4327	0.1282	-0.6121	0.6252	0.5113	-0.1661	-0.2482	-0.2049	-0.0903	0.0379	-0.1309	0.0334	0.0139	0.0369	-0.125	0.0882	-22.7106	66.9561	-35.5301
23	4.818	0.5219	-1.4706	15.3644	-1.1916	0.7881	-0.022	0.1431	0.5211	-0.0711	-0.0033	0.3033	-0.1235	-0.3624	0.0254	-0.0537	0.0268	-0.0136	0.0694	-0.0461	0.0627	-29.8147	65.8053	-39.7997
24	6.8894	0.6859	0.4227	11.6069	7.7007	5.1093	-0.3735	0.7935	-0.6353	0.5279	0.1835	-0.0986	1.4197	0.772	0.1901	0.4728	0.0115	0.0392	-0.0054	-0.0158	0.0346	-24.1787	79.77	-25.0745

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	257 - 275
2	X-RAY DIFFRACTION	2	A	276 - 318
3	X-RAY DIFFRACTION	3	A	319 - 340
4	X-RAY DIFFRACTION	4	A	341 - 352
5	X-RAY DIFFRACTION	5	A	353 - 373
6	X-RAY DIFFRACTION	6	A	374 - 384
7	X-RAY DIFFRACTION	7	B	257 - 264
8	X-RAY DIFFRACTION	8	B	265 - 273
9	X-RAY DIFFRACTION	9	B	274 - 301
10	X-RAY DIFFRACTION	10	B	302 - 338
11	X-RAY DIFFRACTION	11	B	339 - 360
12	X-RAY DIFFRACTION	12	B	361 - 374
13	X-RAY DIFFRACTION	13	C	257 - 264
14	X-RAY DIFFRACTION	14	C	265 - 275
15	X-RAY DIFFRACTION	15	C	276 - 299
16	X-RAY DIFFRACTION	16	C	300 - 354
17	X-RAY DIFFRACTION	17	C	355 - 369
18	X-RAY DIFFRACTION	18	C	370 - 386
19	X-RAY DIFFRACTION	19	D	257 - 275
20	X-RAY DIFFRACTION	20	D	276 - 300
21	X-RAY DIFFRACTION	21	D	301 - 340
22	X-RAY DIFFRACTION	22	D	341 - 356
23	X-RAY DIFFRACTION	23	D	357 - 369
24	X-RAY DIFFRACTION	24	D	370 - 385

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Jul 12, 2017. Major update of PDB

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Yorodumi