PDB-4ayz: X-ray Structure of human SOUL

ID or keywords:

Entry

Database: PDB / ID: 4ayz

Title

X-ray Structure of human SOUL

Components

(HEME-BINDING PROTEIN 2) x 2

Keywords

APOPTOSIS / HEME BINDING PROTEIN

Function / homology

Function and homology information

azurophil granule lumen /

heme binding / Neutrophil degranulation /

mitochondrion / extracellular exosome / extracellular region /

cytoplasm
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.5 Å

Authors

Freire, F. / Carvalho, A.L. / Aveiro, S.S. / Charbonnier, P. / Moulis, J.M. / Romao, M.J. / Goodfellow, B.J. / Macedo, A.L.

Citation

Journal: To be Published
Title: Human Soul: A Heme-Binding or a Bh3 Domain-Containing Protein
Authors: Freire, F. / Carvalho, A.L. / Aveiro, S.S. / Charbonnier, P. / Moulis, J.M. / Romao, M.J. / Goodfellow, B.J. / Macedo, A.L.

History

Deposition	Jun 22, 2012	Deposition site: PDBE / Processing site: PDBE
Supersession	Jul 11, 2012	ID: 2YC9
Revision 1.0	Jul 11, 2012	Provider: repository / Type: Initial release

Remark 650

HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

Remark 700

SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ayz.cif.gz	147.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4ayz.ent.gz	125.3 KB	Display	PDB format
PDBx/mmJSON format	4ayz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ay/4ayz ftp://data.pdbj.org/pub/pdb/validation_reports/ay/4ayz	HTTPS FTP

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Related structure data

Related structure data	4b0yC C: citing same article (ref.)
Similar structure data	3mmi-1 2vv8-d 6yt1-d 4hkk-d 4arq-2 2ibg-1 2i1o-d 1ytd-d 4arm-1 1jbb-d 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

Deposited unit

A: HEME-BINDING PROTEIN 2

B: HEME-BINDING PROTEIN 2

46.8 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)	146.440, 146.440, 133.040
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	180
Space group name H-M	P6₂22

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	5	A	19 - 198
2	1	1	5	B	19 - 198

#1: Protein	HEME-BINDING PROTEIN 2 / HSOUL / PLACENTAL PROTEIN 23 / PP23 / PROTEIN SOUL Mass: 23396.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTYB12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ER2566 / References: UniProt: Q9Y5Z4
#2: Protein	HEME-BINDING PROTEIN 2 / HSOUL / PLACENTAL PROTEIN 23 / PP23 / PROTEIN SOUL Mass: 23396.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTYB12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ER2566 / References: UniProt: Q9Y5Z4
Sequence details	ALA MET HIS RESIDUES IN N-TERMINAL ARE FROM THE EXPRESSION SYSTEM

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.4 Å³/Da / Density % sol: 72 % / Description: NONE
Crystal grow	pH: 5.6 / Details: 1.8 M NA/K PHOSPHATE BUFFER 5.6

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9793
Detector	Type: ADSC CCD / Detector: CCD / Date: Mar 13, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 3.5→50 Å / Num. obs: 11094 / % possible obs: 100 % / Observed criterion σ(I): 4.1 / Redundancy: 13.6 % / R_merge(I) obs: 0.24 / Net I/σ(I): 11
Reflection shell	Resolution: 3.5→3.69 Å / Redundancy: 14.1 % / R_merge(I) obs: 0.98 / Mean I/σ(I) obs: 4.1 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
MOSFLM		data reduction
SCALA		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 3.5→50 Å / Cor.coef. F_o:F_c: 0.894 / Cor.coef. F_o:F_c free: 0.854 / SU B: 56.814 / SU ML: 0.395 / Cross valid method: THROUGHOUT / ESU R: 1.071 / ESU R Free: 0.516
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27038	1082	9.8 %	RANDOM
R_work	0.23435	-	-	-
obs	0.23799	9915	98.84 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 92.35 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.51 Å²	-0.25 Å²	0 Å²
2-	-	-0.51 Å²	0 Å²
3-	-	-	0.76 Å²

Refinement step

Cycle: LAST / Resolution: 3.5→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2729	0	0	0	2729

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	2802
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.031	1.948	3839
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr
X-RAY DIFFRACTION	r_gen_planes_refined
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	712	medium positional	0.65	0.5
2	B	712	medium positional	0.65	0.5
1	A	590	loose positional	0.87	5
2	B	590	loose positional	0.87	5

LS refinement shell

Resolution: 3.5→3.59 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.331	80	-
R_work	0.284	688	-
obs	-	-	97.09 %

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	0.9195	-1.7391	1.8069	3.4679	-3.6089	3.757	-0.5424	-0.3314	0.3515	0.8147	0.2499	-0.3987	-0.8484	-0.3759	0.2924	0.4872	0.1803	-0.1031	0.8027	-0.4015	0.6301	32.6802	64.508	95.2178
2	7.1469	-1.4756	-4.1644	0.3168	0.8771	2.4513	-0.2675	-0.0336	-0.485	0.1222	-0.0242	0.1262	0.2429	0.013	0.2916	0.503	0.0729	0.1087	0.1529	-0.0858	0.2304	32.3098	47.3041	95.8236
3	25.8789	11.605	-9.5805	5.2063	-4.2969	3.5501	0.7524	-0.2109	1.6016	0.3259	-0.1059	0.748	-0.3243	0.0476	-0.6466	0.888	0.1377	0.1751	0.8398	0.0306	0.8121	39.2801	36.2174	102.0881
4	5.6427	-2.0213	3.5628	5.7969	-5.2388	5.4154	0.1996	-0.4852	0.1041	0.4086	-0.0719	0.2057	-0.0929	-0.0414	-0.1277	0.3932	0.1272	0.024	0.1464	-0.0364	0.0333	30.8341	45.371	90.1679
5	2.9878	-1.6836	-0.3112	7.2677	0.8928	1.7712	0.0359	0.0822	0.0078	-0.2922	-0.0359	-0.1025	-0.1897	0.1732	0	0.1405	0.102	-0.0077	0.1877	0.0505	0.0881	29.6617	56.2137	74.1974
6	4.8388	-3.623	-4.4322	5.3027	2.3202	5.1304	-0.0969	0.2277	-0.2659	-0.2716	0.0292	0.525	0.365	-0.3605	0.0677	0.1375	0.048	-0.0389	0.1839	0.0335	0.061	30.2985	47.2176	78.2257
7	3.47	0.2601	-0.3435	7.987	-0.5051	7.3249	-0.1089	-0.1087	-0.4725	-0.2523	-0.1972	0.4198	0.7803	-0.9626	0.3061	0.1122	-0.0623	0.0018	0.1985	-0.0262	0.2852	20.0082	53.265	80.3373
8	5.6555	2.5762	-5.0332	11.9288	-1.0118	7.3697	-0.2332	0.6185	0.0602	0.1391	0.0841	-0.9543	0.2994	-0.1302	0.1491	0.1848	0.109	-0.0901	0.2414	0.0209	0.1593	42.8323	39.9473	83.5825
9	21.9546	-1.9111	-3.9168	13.2816	-9.1418	7.7371	0.1795	-0.7548	-0.2934	-1.2284	0.3196	0.5214	1.1716	-0.2093	-0.499	0.891	-0.2147	-0.1513	0.1725	0.1488	0.4479	37.0115	29.278	87.3681
10	5.1022	-0.5726	0.2194	10.8257	2.0634	2.6468	0.1372	-0.1748	0.0336	0.4271	-0.1601	-0.5026	0.1044	0.0057	0.0229	0.1115	0.1096	-0.011	0.1748	0.0205	0.0303	37.6494	46.9223	85.0992
11	10.1232	4.1719	4.7878	3.0205	2.4695	5.4586	-0.4759	1.7237	-0.109	-0.3996	0.1783	-0.4943	-0.7079	0.0203	0.2976	0.3896	0.0306	0.1458	0.6363	0.0358	0.3176	55.5523	27.6964	46.1655
12	8.5578	19.6799	15.4871	75.2343	39.2259	28.4845	-0.0729	0.3172	0.2926	-0.9424	-0.7364	2.3005	-0.234	0.4754	0.8093	0.8665	0.0001	0.0587	0.7296	-0.1433	0.6351	41.5135	36.7263	41.4056
13	4.4757	-3.4139	-0.7253	6.7675	0.1311	5.1922	0.1643	0.1936	-0.1122	-0.4813	-0.0537	-0.1604	-0.1455	-0.2489	-0.1106	0.1495	-0.0133	0.0707	0.0268	-0.0337	0.1459	51.0477	25.9224	55.7871
14	6.2926	-5.4089	-0.8149	10.998	6.1119	5.4501	-0.1219	-0.2341	0.4292	-0.0311	0.3291	-0.2231	-0.2129	0.34	-0.2072	0.3297	0.02	-0.0118	0.1519	-0.1116	0.2685	61.1105	28.3336	67.5901
15	3.0836	-2.0802	7.2828	1.4203	-4.9598	17.3357	0.2381	0.4004	-0.0555	-0.0548	-0.1605	0.0474	0.2277	0.7978	-0.0776	0.4083	0.1821	0.0714	0.3808	-0.0429	0.559	68.5729	18.1476	58.4631
16	4.6844	-3.6587	-3.098	5.6307	4.354	5.765	-0.4073	-0.3277	-0.2027	0.2892	0.0917	0.1778	0.4193	-0.0346	0.3156	0.1958	0.0675	-0.0522	0.0688	-0.0546	0.1429	53.5134	22.9938	62.2417
17	17.2285	-6.1069	10.9674	7.387	-5.8895	14.5344	0.3805	-0.5876	0.0331	0.0943	0.0858	0.0798	0.699	-0.4216	-0.4664	0.189	0.0382	0.0611	0.0831	-0.0075	0.2233	56.3367	16.6117	62.2117
18	15.0124	2.2451	3.529	2.9786	3.8822	5.2766	0.5446	0.1162	0.3973	0.2021	-0.5682	0.0012	0.0273	-0.5619	0.0236	0.6045	-0.0368	-0.0027	0.3626	0.0115	0.0638	49.2274	36.7204	54.4545
19	9.9156	2.1791	-2.8086	4.1708	0.1109	0.977	0.4259	-0.1097	0.7377	-0.1177	-0.1649	-0.1547	-0.1314	-0.1411	-0.261	0.4431	0.059	0.0202	0.6005	0.0015	0.1855	41.8694	40.2442	58.3814
20	10.2011	0.5015	-0.4641	5.4184	-1.8653	7.5825	0.3905	0.4112	0.2054	-0.306	-0.1421	-0.2552	-0.3835	0.1069	-0.2484	0.2786	0.0785	0.0194	0.0709	-0.0598	0.1657	50.1368	32.9976	57.1003

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	15 - 21
2	X-RAY DIFFRACTION	2	A	22 - 28
3	X-RAY DIFFRACTION	3	A	29 - 36
4	X-RAY DIFFRACTION	4	A	37 - 50
5	X-RAY DIFFRACTION	5	A	51 - 85
6	X-RAY DIFFRACTION	6	A	86 - 116
7	X-RAY DIFFRACTION	7	A	117 - 134
8	X-RAY DIFFRACTION	8	A	135 - 162
9	X-RAY DIFFRACTION	9	A	163 - 172
10	X-RAY DIFFRACTION	10	A	173 - 198
11	X-RAY DIFFRACTION	11	B	19 - 28
12	X-RAY DIFFRACTION	12	B	29 - 37
13	X-RAY DIFFRACTION	13	B	38 - 55
14	X-RAY DIFFRACTION	14	B	56 - 73
15	X-RAY DIFFRACTION	15	B	74 - 87
16	X-RAY DIFFRACTION	16	B	88 - 120
17	X-RAY DIFFRACTION	17	B	121 - 134
18	X-RAY DIFFRACTION	18	B	135 - 146
19	X-RAY DIFFRACTION	19	B	147 - 168
20	X-RAY DIFFRACTION	20	B	169 - 198

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