PDB-2qzt: Crystal Structure of Sterol Carrier Protein 2 Like 2 (SCP2-L2) fr...

ID or keywords:

Entry

Database: PDB / ID: 2qzt

Title

Crystal Structure of Sterol Carrier Protein 2 Like 2 (SCP2-L2) from Aedes Aegypti

Components

Sterol carrier protein 2-like 2

Keywords

LIPID TRANSPORT / Sterol Carrier /

Mosquito /

Fatty Acid /

Palmitic acid /

cholesterol

Function / homology

Function and homology information

Lipid-binding protein POX18/UbiT/NSL-TP1 / SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology

Biological species

Aedes aegypti (yellow fever mosquito)

Method

X-RAY DIFFRACTION /

MIR / Resolution: 1.7 Å

Authors

Dyer, D.H. / Lan, Q. / Forest, K.T.

Citation

Journal: J.Lipid Res. / Year: 2008
Title: Three-dimensional structure/function analysis of SCP-2-like2 reveals differences among SCP-2 family members.
Authors: Dyer, D.H. / Wessely, V. / Forest, K.T. / Lan, Q.

History

Deposition	Aug 17, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 11, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software
Revision 1.3	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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	2qzt.cif.gz	59.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2qzt.ent.gz	42.8 KB	Display	PDB format
PDBx/mmJSON format	2qzt.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qz/2qzt ftp://data.pdbj.org/pub/pdb/validation_reports/qz/2qzt	HTTPS FTP

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Related structure data

Related structure data	3bdqC 1pz4 C: citing same article (ref.)
Similar structure data	3to1-2 3rk6-2 4ef2-2 1th8-d 3rk6-1 4csv-d 2oz6-d 4iop-d 4edj-1 1oey-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #147 - Mar 2012 Rhodopsin similarity (1) #100 - Apr 2008 Adrenergic Receptors similarity (1) #164 - Aug 2013 Serotonin Receptor similarity (1) #171 - Mar 2014 Neurotransmitter Transporters similarity (1) #27 - Mar 2002 Bacteriorhodopsin similarity (1)

Deposited unit

A: Sterol carrier protein 2-like 2

B: Sterol carrier protein 2-like 2

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	45.36, 56.44, 50.61
Angle α, β, γ (deg.)	90.000, 119.400, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Details

It is a dimer in the asymetric unit which is suspected to be the biological unit.

#1: Protein	Sterol carrier protein 2-like 2 Mass: 11680.525 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Gene: Sterol Carrier Protein 2 Like 2 / Plasmid: pGEX-4T-2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q0GY13
#2: Chemical	ChemComp-PLM / PALMITIC ACID / Palmitic acid Mass: 256.424 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₆H₃₂O₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.42 Å³/Da / Density % sol: 49.09 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2 microl protein @ 10mg/ml was mixed with 2microl mother liquor consisting of 1.6 M sodium citrate, 5% glycerol, 100 mM Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	263	1
2		1
3		1

Diffraction source

Source:

ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418

Detector

Type: BRUKER PROTEUM / Detector: CCD / Date: Jul 13, 2006 / Details: Montel 200 multilayer graded mirrors

Radiation

Monochromator: graded mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Av σ(I) over netI: 25.8 / Number: 84952 / R_merge(I) obs: 0.073 / Χ²: 1 / D res high: 1.7 Å / D res low: 30 Å / Num. obs: 24343 / % possible obs: 98.8 / Redundancy: 3.5 %

ID
1
2
3

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
3.66	30	100	1	0.059	0.725	6.6
2.91	3.66	99.8	1	0.072	1.035	5.7
2.54	2.91	99.5	1	0.101	1.157	5.3
2.31	2.54	99.9	1	0.112	1.056	4.3
2.14	2.31	99.8	1	0.08	1.096	2.9
2.02	2.14	99.5	1	0.08	1.078	2.5
1.91	2.02	99.2	1	0.081	1.184	2.2
1.83	1.91	98.9	1	0.092	1.136	1.9
1.76	1.83	97.7	1	0.106	0.963	1.7
1.7	1.76	93.8	1	0.117	0.806	1.5
3.66	30	100	2	0.059	0.725	6.6
2.91	3.66	99.8	2	0.072	1.035	5.7
2.54	2.91	99.5	2	0.101	1.157	5.3
2.31	2.54	99.9	2	0.112	1.056	4.3
2.14	2.31	99.8	2	0.08	1.096	2.9
2.02	2.14	99.5	2	0.08	1.078	2.5
1.91	2.02	99.2	2	0.081	1.184	2.2
1.83	1.91	98.9	2	0.092	1.136	1.9
1.76	1.83	97.7	2	0.106	0.963	1.7
1.7	1.76	93.8	2	0.117	0.806	1.5
3.66	30	100	3	0.059	0.725	6.6
2.91	3.66	99.8	3	0.072	1.035	5.7
2.54	2.91	99.5	3	0.101	1.157	5.3
2.31	2.54	99.9	3	0.112	1.056	4.3
2.14	2.31	99.8	3	0.08	1.096	2.9
2.02	2.14	99.5	3	0.08	1.078	2.5
1.91	2.02	99.2	3	0.081	1.184	2.2
1.83	1.91	98.9	3	0.092	1.136	1.9
1.76	1.83	97.7	3	0.106	0.963	1.7
1.7	1.76	93.8	3	0.117	0.806	1.5

Reflection

Resolution: 1.7→30 Å / Num. obs: 24343 / % possible obs: 98.8 % / Redundancy: 3.5 % / B_iso Wilson estimate: 19 Å² / R_sym value: 0.073 / Χ²: 0.997 / Net I/σ(I): 25.8

Reflection shell

Resolution: 1.7→1.76 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 4.9 / Num. unique all: 2304 / R_sym value: 0.117 / Χ²: 0.806 / % possible all: 93.8

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Phasing

Phasing

Method:

MIR

Phasing set

ID
1
2
3
4

Phasing MIR der

Native set-ID: 1 / Resolution: 2.5→19.79 Å

ID	Der set-ID	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	1	0	0	7301	481
ISO_2	2	1.342	1.474	7045	224
ISO_3	3	0.662	0.712	5102	165
ISO_4	4	0.205	0.212	5642	201

Phasing MIR der shell

Highest resolution (Å)	Lowest resolution (Å)	Der-ID	Power acentric	Power centric	Reflection acentric	Reflection centric
9.79	19.79	ISO_1	0	0	98	24
7.39	9.79	ISO_1	0	0	157	23
6.18	7.39	ISO_1	0	0	191	24
5.42	6.18	ISO_1	0	0	237	25
4.88	5.42	ISO_1	0	0	261	22
4.48	4.88	ISO_1	0	0	283	25
4.16	4.48	ISO_1	0	0	318	22
3.91	4.16	ISO_1	0	0	334	25
3.69	3.91	ISO_1	0	0	354	27
3.51	3.69	ISO_1	0	0	369	21
3.35	3.51	ISO_1	0	0	402	25
3.21	3.35	ISO_1	0	0	417	23
3.09	3.21	ISO_1	0	0	430	23
2.98	3.09	ISO_1	0	0	446	26
2.88	2.98	ISO_1	0	0	458	20
2.79	2.88	ISO_1	0	0	494	28
2.71	2.79	ISO_1	0	0	485	21
2.63	2.71	ISO_1	0	0	516	30
2.56	2.63	ISO_1	0	0	526	17
2.5	2.56	ISO_1	0	0	525	30
9.79	19.79	ISO_2	2.792	3.765	98	12
7.39	9.79	ISO_2	2.285	1.487	156	11
6.18	7.39	ISO_2	2.494	1.328	189	11
5.42	6.18	ISO_2	2.245	1.587	236	13
4.88	5.42	ISO_2	1.92	1.745	256	10
4.48	4.88	ISO_2	1.639	1.524	277	11
4.16	4.48	ISO_2	1.406	1.28	315	12
3.91	4.16	ISO_2	1.41	1.191	328	14
3.69	3.91	ISO_2	1.183	0.879	349	10
3.51	3.69	ISO_2	1.128	0.491	362	14
3.35	3.51	ISO_2	1.112	0.808	396	12
3.21	3.35	ISO_2	1.067	0.81	414	9
3.09	3.21	ISO_2	0.942	0.672	425	11
2.98	3.09	ISO_2	0.929	0.824	441	16
2.88	2.98	ISO_2	0.879	0.629	453	7
2.79	2.88	ISO_2	0.782	0.732	492	14
2.71	2.79	ISO_2	0.698	0.613	483	12
2.63	2.71	ISO_2	0.659	0.603	512	15
2.56	2.63	ISO_2	0.561	0.536	494	4
2.5	2.56	ISO_2	0.512	0.459	369	6
9.79	19.79	ISO_3	1.525	2.202	98	12
7.39	9.79	ISO_3	1.373	0.939	157	12
6.18	7.39	ISO_3	1.303	0.523	191	11
5.42	6.18	ISO_3	1.102	0.566	237	12
4.88	5.42	ISO_3	0.811	0.553	261	9
4.48	4.88	ISO_3	0.631	0.576	283	10
4.16	4.48	ISO_3	0.521	0.58	317	10
3.91	4.16	ISO_3	0.563	0.492	333	12
3.69	3.91	ISO_3	0.475	0.321	354	7
3.51	3.69	ISO_3	0.48	0.28	367	12
3.35	3.51	ISO_3	0.504	0.243	400	10
3.21	3.35	ISO_3	0.526	0.508	414	8
3.09	3.21	ISO_3	0.534	0.438	428	11
2.98	3.09	ISO_3	0.521	0.346	439	13
2.88	2.98	ISO_3	0.533	0.19	454	6
2.79	2.88	ISO_3	0.538	0.447	369	10
2.71	2.79	ISO_3	0	0	0	0
2.63	2.71	ISO_3	0	0	0	0
2.56	2.63	ISO_3	0	0	0	0
2.5	2.56	ISO_3	0	0	0	0
9.79	19.79	ISO_4	0.423	0.325	98	12
7.39	9.79	ISO_4	0.543	0.369	157	12
6.18	7.39	ISO_4	0.502	0.371	191	11
5.42	6.18	ISO_4	0.401	0.335	236	13
4.88	5.42	ISO_4	0.295	0.237	257	10
4.48	4.88	ISO_4	0.208	0.165	281	11
4.16	4.48	ISO_4	0.163	0.134	316	12
3.91	4.16	ISO_4	0.143	0.14	332	13
3.69	3.91	ISO_4	0.115	0.081	352	9
3.51	3.69	ISO_4	0.098	0.077	366	14
3.35	3.51	ISO_4	0.082	0.055	397	12
3.21	3.35	ISO_4	0.069	0.06	417	10
3.09	3.21	ISO_4	0.057	0.041	429	12
2.98	3.09	ISO_4	0.047	0.037	446	16
2.88	2.98	ISO_4	0.041	0.029	456	7
2.79	2.88	ISO_4	0.032	0.022	478	14
2.71	2.79	ISO_4	0.026	0.019	419	12
2.63	2.71	ISO_4	0.024	0.023	14	1
2.56	2.63	ISO_4	0	0	0	0
2.5	2.56	ISO_4	0	0	0	0

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
SOLOMON		phasing
REFMAC		refinement
PDB_EXTRACT	2	data extraction
PROTEUM PLUS	PLUS	data collection

Refinement

Method to determine structure:

MIR / Resolution: 1.7→25 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.916 / SU B: 4.42 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.236	1225	5.1 %	RANDOM
R_work	0.198	-	-	-
obs	0.2	24120	98.09 %	-
all	-	24589	-	-

Solvent computation

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

Displacement parameters

B_iso mean: 17.36 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.47 Å²	0 Å²	-0.54 Å²
2-	-	0.61 Å²	0 Å²
3-	-	-	-0.68 Å²

Refine analyze

	Free	Obs
Luzzati coordinate error	0.118 Å	0.121 Å

Refinement step

Cycle: LAST / Resolution: 1.7→25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1629	0	54	204	1887

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	1694
X-RAY DIFFRACTION	r_angle_refined_deg	1.425	2.018	2274
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.037	5	218
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.334	26.071	56
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.737	15	316
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	8.988	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	281
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	1168
X-RAY DIFFRACTION	r_nbd_refined	0.231	0.3	809
X-RAY DIFFRACTION	r_nbtor_refined	0.323	0.5	1156
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.199	0.5	285
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.141	0.3	36
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.261	0.5	17
X-RAY DIFFRACTION	r_mcbond_it	1.353	2	1111
X-RAY DIFFRACTION	r_mcangle_it	1.826	3	1747
X-RAY DIFFRACTION	r_scbond_it	1.537	2	641
X-RAY DIFFRACTION	r_scangle_it	2.276	3	527

LS refinement shell

Resolution: 1.7→1.744 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.235	80	-
R_work	0.22	1545	-
obs	-	1625	89.73 %

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