PDB-2wh5: Crystal structure of human acyl-CoA binding domain 4 complexed wi...

ID or keywords:

Entry

Database: PDB / ID: 2wh5

Title

Crystal structure of human acyl-CoA binding domain 4 complexed with stearoyl-CoA

Components

ACYL-COA-BINDING DOMAIN-CONTAINING PROTEIN 4

Keywords

LIPID BINDING PROTEIN /

ALTERNATIVE SPLICING /

FATTY ACID METABOLISM / LIPID TRANSPORT /

ACYL-COA BINDING

Function / homology

Function and homology information

Peroxisomal lipid metabolism / fatty-acyl-CoA binding /

lipid binding
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Yue, W.W. / Shafqat, N. / Ugochukwu, E. / Savitsky, P. / Johansson, C. / Salah, E. / Roos, A.K. / Chaikuad, A. / von Delft, F. / Arrowsmith, C. ...

Citation

Journal: To be Published
Title: Crystal Structure of Human Acyl-Coa Binding Domain 4
Authors: Shafqat, N. / Yue, W.W. / Oppermann, U.

History

Deposition	Apr 30, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 28, 2009	Provider: repository / Type: Initial release
Revision 1.1	Dec 5, 2012	Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2	Sep 25, 2013	Group: Advisory / Non-polymer description / Source and taxonomy
Revision 1.3	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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	2wh5.cif.gz	241.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2wh5.ent.gz	200.4 KB	Display	PDB format
PDBx/mmJSON format	2wh5.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/wh/2wh5 ftp://data.pdbj.org/pub/pdb/validation_reports/wh/2wh5	HTTPS FTP

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Related structure data

Related structure data	1hbkS S: Starting model for refinement
Similar structure data	6o6i-d 3nju-d 3osh-d 2wq5-d 5dkh-2 4dbk-d 2bp2-d 5e7d-3 5dkc-d 6uwo-2 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) 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

1hbkS

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	#37 - Jan 2003 Serum Albumin similarity (1) #134 - Feb 2011 Integrin similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: ACYL-COA-BINDING DOMAIN-CONTAINING PROTEIN 4

B: ACYL-COA-BINDING DOMAIN-CONTAINING PROTEIN 4

C: ACYL-COA-BINDING DOMAIN-CONTAINING PROTEIN 4

D: ACYL-COA-BINDING DOMAIN-CONTAINING PROTEIN 4

E: ACYL-COA-BINDING DOMAIN-CONTAINING PROTEIN 4

F: ACYL-COA-BINDING DOMAIN-CONTAINING PROTEIN 4

hetero molecules

82.3 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ACYL-COA-BINDING DOMAIN-CONTAINING PROTEIN 4

hetero molecules

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

2

B: ACYL-COA-BINDING DOMAIN-CONTAINING PROTEIN 4

hetero molecules

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

3

C: ACYL-COA-BINDING DOMAIN-CONTAINING PROTEIN 4

hetero molecules

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

4

D: ACYL-COA-BINDING DOMAIN-CONTAINING PROTEIN 4

hetero molecules

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

5

E: ACYL-COA-BINDING DOMAIN-CONTAINING PROTEIN 4

hetero molecules

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

6

F: ACYL-COA-BINDING DOMAIN-CONTAINING PROTEIN 4

hetero molecules

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

Unit cell

Length a, b, c (Å)	85.060, 95.100, 119.740
Angle α, β, γ (deg.)	90.00, 110.28, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	ACYL-COA-BINDING DOMAIN-CONTAINING PROTEIN 4 Mass: 12145.884 Da / Num. of mol.: 6 / Fragment: ACYL-COA BINDING DOMAIN, RESIDUES 7-110 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q8NC06
#2: Chemical	ChemComp-STE / STEARIC ACID / Stearic acid Mass: 284.477 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₈H₃₆O₂
#3: Chemical	ChemComp-ST9 / STEAROYL-COENZYME A / Stearoyl-CoA Mass: 1033.996 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃₉H₇₀N₇O₁₇P₃S
#4: Chemical	ChemComp-COA / COENZYME A / Coenzyme A Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 89 / 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: 6.24 Å³/Da / Density % sol: 80.3 % / Description: NONE
Crystal grow	Details: 0.24M K_THIOCYANATE; 26W/V PEG_3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
Detector	Type: MARRESEARCH / Detector: CCD / Date: Mar 27, 2009 / Details: OSMIC
Radiation	Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.55→79.78 Å / Num. obs: 58524 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 4 % / B_iso Wilson estimate: 47.07 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 4.5
Reflection shell	Resolution: 2.55→2.6 Å / Redundancy: 3 % / R_merge(I) obs: 0.48 / Mean I/σ(I) obs: 2 / % possible all: 91

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HBK

1hbk

Resolution: 2.6→42.528 Å / SU ML: 1.07 / σ(F): 1.03 / Phase error: 23.7 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.2365	2912	2.8 %
R_work	0.206	-	-
obs	0.2069	105269	97.28 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 34.676 Å² / k_sol: 0.322 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.0124 Å²	0 Å²	-7.8959 Å²
2-	-	2.9725 Å²	0 Å²
3-	-	-	-0.838 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→42.528 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4278	0	584	89	4951

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	4998
X-RAY DIFFRACTION	f_angle_d	1.481	6764
X-RAY DIFFRACTION	f_dihedral_angle_d	22.581	2172
X-RAY DIFFRACTION	f_chiral_restr	0.07	604
X-RAY DIFFRACTION	f_plane_restr	0.02	784

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 (%)
2.6-2.6426	0.2825	91	0.2758	4173	X-RAY DIFFRACTION	82
2.6426-2.6882	0.3354	124	0.2831	4296	X-RAY DIFFRACTION	87
2.6882-2.7371	0.3608	134	0.2862	4613	X-RAY DIFFRACTION	91
2.7371-2.7897	0.2829	102	0.2598	4871	X-RAY DIFFRACTION	97
2.7897-2.8466	0.2562	159	0.2521	4903	X-RAY DIFFRACTION	99
2.8466-2.9085	0.304	139	0.2443	4941	X-RAY DIFFRACTION	99
2.9085-2.9762	0.2497	163	0.2351	4901	X-RAY DIFFRACTION	99
2.9762-3.0506	0.278	152	0.2452	4995	X-RAY DIFFRACTION	99
3.0506-3.133	0.2817	132	0.2393	4944	X-RAY DIFFRACTION	99
3.133-3.2252	0.2354	140	0.2314	4919	X-RAY DIFFRACTION	99
3.2252-3.3292	0.2337	147	0.2187	4981	X-RAY DIFFRACTION	99
3.3292-3.4482	0.2544	133	0.207	4994	X-RAY DIFFRACTION	99
3.4482-3.5862	0.2626	143	0.2125	4945	X-RAY DIFFRACTION	99
3.5862-3.7493	0.2136	149	0.1864	5018	X-RAY DIFFRACTION	99
3.7493-3.9468	0.2251	120	0.1714	4952	X-RAY DIFFRACTION	99
3.9468-4.1939	0.2166	120	0.1591	4984	X-RAY DIFFRACTION	99
4.1939-4.5174	0.1696	190	0.1388	5004	X-RAY DIFFRACTION	99
4.5174-4.9714	0.1671	158	0.136	4967	X-RAY DIFFRACTION	100
4.9714-5.6893	0.1651	134	0.1547	4991	X-RAY DIFFRACTION	100
5.6893-7.1623	0.2253	162	0.1903	4977	X-RAY DIFFRACTION	100
7.1623-42.5339	0.2161	120	0.1868	4988	X-RAY DIFFRACTION	99

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	0.7595	-0.4877	0.3523	0.6281	-1.0615	1.1324	-0.085	0.1607	0.3453	0.2792	0.1264	0.459	-0.7372	-0.2841	0.0132	0.6172	0.119	-0.0014	0.4201	0.2159	0.4517	18.1521	96.1864	66.007
2	3.5819	-0.2938	2.4444	0.6975	0.1972	0.7212	-0.2409	1.2016	0.2141	-0.2981	0.3771	0.2982	0.5076	-0.1852	-0.0917	0.6318	-0.1255	-0.2523	0.7349	0.2528	0.5026	13.7605	82.7249	60.6173
3	0.9787	0.1817	0.5644	1.4988	-0.2398	2.2999	-0.1156	-0.1639	0.1082	-0.1247	-0.0809	0.2686	-0.404	-0.0586	0.1495	0.2385	0.0066	-0.0077	0.1775	0.0314	0.2448	20.5717	83.6784	79.3207
4	2.1469	0.2119	2.0456	1.245	-1.0318	2.9245	0.0534	0.4093	0.61	0.1891	-0.6341	-0.1703	0.103	0.7989	0.4939	0.252	-0.0243	-0.0294	0.2122	0.1232	0.2689	27.0311	90.4224	65.8802
5	0.4199	0.1261	0.4392	0.8269	0.5585	0.8409	-0.2949	0.2366	0.0087	-0.5247	0.3004	0.0334	-0.4192	0.1187	0.0084	0.6006	-0.0605	-0.0511	0.3209	-0.1037	0.3735	30.6517	50.0852	57.1897
6	0.2884	0.1209	0.0588	1.3091	-0.4462	0.5467	0.3779	-0.1726	0.2852	-0.8527	-0.0664	0.672	0.2232	-0.3395	0.0004	0.7567	0.2133	-0.3496	0.5578	-0.2113	0.7559	17.5204	57.9241	56.9667
7	0.0577	-0.6649	0.0217	1.5581	0.2222	1.1354	0.2212	0.0311	-0.0429	0.0192	-0.3071	0.3444	-0.0686	-0.0059	0.0552	0.217	-0.019	0.0133	0.2088	-0.0513	0.2699	29.7156	59.8658	72.9671
8	1.4492	-0.5433	1.597	2.5252	-0.3865	3.2621	-0.1552	-0.2317	0.3003	-0.2052	-0.4482	-0.0702	0.3391	-0.3228	-0.7447	0.1911	-0.0568	-0.0346	0.0477	-0.1777	0.0109	24.775	46.2627	65.0997
9	0.0328	0.6396	0.7491	1.0964	0.1302	0.6016	-0.0868	0.4737	0.2135	0.7078	0.1224	-0.4281	-0.1596	0.2109	0.0416	0.3873	-0.0342	-0.0738	0.1736	-0.1122	0.3828	39.2687	85.0461	102.4572
10	-0.2381	0.1365	-0.057	0.0093	0.0098	0.2984	-0.0933	-0.1646	0.0938	0.0358	-0.0452	-0.1556	0.2957	0.3624	-0.0495	0.7962	0.2058	-0.2223	0.5682	-0.2178	0.4779	47.5896	72.7726	106.1161
11	0.4991	0.2131	-0.1057	0.7535	0.6838	0.8037	-0.1819	0.0105	0.0428	0.0993	0.0964	-0.1249	0.3228	-0.134	0.0901	0.2466	-0.0134	0.0062	0.1516	-0.0184	0.1485	34.6688	71.7658	90.7249
12	0.7742	0.4523	0.6898	0.6084	0.6986	0.697	0.309	-0.0862	0.0928	0.3323	-0.3233	0.0159	0.5026	-0.0338	-0.0873	0.393	-0.0074	0.0143	0.2618	-0.0928	0.1703	32.0699	77.5796	105.8686
13	1.282	-1.3168	-0.682	1.1311	-1.3544	2.0741	0.0342	-0.578	-0.0593	0.1403	0.9255	0.6413	-0.2923	-0.3552	-0.6982	0.5603	-0.1152	-0.0093	0.595	0.2566	0.4807	36.718	37.8674	113.0633
14	-0.7102	0.3849	-0.9733	1.9514	1.8202	-2.3932	0.1829	0.0056	0.2524	0.3227	0.3189	-0.1533	0.8526	-0.3619	-0.3992	0.7929	-0.2396	-0.4293	0.4479	0.1903	0.6514	48.3755	46.389	110.1908
15	0.5095	-0.8555	-0.2549	1.2261	-0.0396	0.6422	0.2596	-0.102	-0.27	-0.7385	-0.0687	0.5342	-0.0122	-0.0398	-0.2625	0.3995	-0.1595	-0.1717	0.1994	0.1334	0.334	32.7569	47.1214	97.804
16	0.079	1.0415	0.2678	1.9194	-0.0007	1.8287	-0.0652	0.3821	0.0896	-0.3508	0.0722	0.5096	0.7303	0.3469	-0.0035	0.634	-0.075	-0.1333	0.3081	0.1702	0.3526	41.0071	33.8883	103.3216
17	0.2668	0.1051	0.2065	0.5005	0.3232	0.0875	0.0908	-0.0151	0.2473	-0.0699	-0.3584	0.5516	0.2455	-0.4255	0.1989	0.2486	-0.141	0.2303	0.6911	-0.1839	0.6182	-8.8534	58.138	86.6337
18	-1.1514	0.5883	-3.2421	-1.8295	-0.281	3.9632	-0.1033	-0.6596	0.2797	-0.2055	-0.8464	-0.0953	-0.1652	-0.9505	0.6349	0.3135	0.0472	-0.0043	1.2126	-0.058	0.4225	-5.1193	63.8457	73.209
19	-0.2986	0.5092	0.007	0.9563	0.4028	0.5008	0.0953	-0.3565	0.2791	0.1048	-0.0104	-0.3096	0.1791	-0.2396	-0.1249	0.1475	-0.0969	0.0708	0.5229	0.0205	0.2255	8.7885	62.8182	87.5409
20	0.8069	2.8812	0.3393	2.0812	-0.0309	1.4132	0.2387	-0.186	1.353	-0.0056	-0.6051	0.8842	-0.0235	0.0941	0.1435	0.2291	-0.0813	0.1917	0.7485	-0.2032	0.5039	-6.7861	68.2901	88.2379
21	0.1934	0.2532	-0.5704	0.5123	-0.3319	0.0008	-0.1318	0.31	-1.0486	0.1227	-0.4553	-0.2682	-0.032	0.498	0.423	0.3026	0.041	0.0957	0.6114	-0.0216	0.8483	67.5128	55.2196	77.479
22	1.7336	1.8362	0.685	0.8348	-0.1885	-0.4444	0.4223	-0.4696	0.0237	0.3205	-0.6434	-0.0518	0.0215	0.6973	0.171	0.2564	-0.1151	-0.083	0.6741	0.0754	0.4166	59.6804	59.9164	89.6079
23	1.3069	0.7201	0.7809	0.3395	0.6376	1.2482	0.0721	0.2358	-0.1942	0.061	0.2704	-0.1076	0.2951	0.1703	-0.3571	0.2341	0.011	0.0396	0.2975	-0.0284	0.3223	48.8001	52.2197	78.5671
24	1.1082	-1.5063	0.9712	0.7393	-0.3985	0.0495	-0.1914	0.1105	0.8532	-0.0378	-0.0776	-0.7471	-0.1353	0.1159	0.1605	0.21	-0.0407	0.097	0.5197	0.0195	0.6296	61.709	63.9671	76.9693

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 11:23)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 24:31)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 32:76)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 77:96)
5	X-RAY DIFFRACTION	5	(CHAIN B AND RESID 11:23)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 24:31)
7	X-RAY DIFFRACTION	7	(CHAIN B AND RESID 32:76)
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESID 77:96)
9	X-RAY DIFFRACTION	9	(CHAIN C AND RESID 11:24)
10	X-RAY DIFFRACTION	10	(CHAIN C AND RESID 25:31)
11	X-RAY DIFFRACTION	11	(CHAIN C AND RESID 32:76)
12	X-RAY DIFFRACTION	12	(CHAIN C AND RESID 77:96)
13	X-RAY DIFFRACTION	13	(CHAIN D AND RESID 11:24)
14	X-RAY DIFFRACTION	14	(CHAIN D AND RESID 25:31)
15	X-RAY DIFFRACTION	15	(CHAIN D AND RESID 32:76)
16	X-RAY DIFFRACTION	16	(CHAIN D AND RESID 77:96)
17	X-RAY DIFFRACTION	17	(CHAIN E AND RESID 11:23)
18	X-RAY DIFFRACTION	18	(CHAIN E AND RESID 24:31)
19	X-RAY DIFFRACTION	19	(CHAIN E AND RESID 32:76)
20	X-RAY DIFFRACTION	20	(CHAIN E AND RESID 77:96)
21	X-RAY DIFFRACTION	21	(CHAIN F AND RESID 11:21)
22	X-RAY DIFFRACTION	22	(CHAIN F AND RESID 22:36)
23	X-RAY DIFFRACTION	23	(CHAIN F AND RESID 37:76)
24	X-RAY DIFFRACTION	24	(CHAIN F AND RESID 77:96)

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