PDB-3zxb: Wild type single insulin-like growth factor binding domain protei...

ID or keywords:

Entry

Database: PDB / ID: 3zxb

Title

Wild type single insulin-like growth factor binding domain protein (SIBD-1) from Cupiennius salei

Components

SINGLE INSULIN-LIKE GROWTH FACTOR-BINDING DOMAIN PROTEIN-1

Keywords

SIGNALING /

IGFBP / INSULIN BINDING DOMAIN

Function / homology

Function and homology information

insulin-like growth factor binding /

regulation of cell growth /

innate immune response / extracellular region
Similarity search - Function

Biological species

CUPIENNIUS SALEI (spider)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.55 Å

Authors

Widmer, C. / Baumann, U.

Citation

Journal: Proteins / Year: 2012
Title: Structural and Biochemical Characterization of Native and Recombinant Single Insulin-Like Growth Factor-Binding Domain Protein (Sibd-1) from the Central American Hunting Spider Cupiennius Salei (Ctenidae).
Authors: Trachsel, C. / Widmer, C. / Kampfer, U. / Buhr, C. / Baumann, T. / Kuhn-Nentwig, L. / Schurch, S. / Schaller, J. / Baumann, U.

History

Deposition	Aug 9, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 6, 2012	Provider: repository / Type: Initial release
Revision 1.1	Aug 8, 2012	Group: Database references
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3zxb.cif.gz	111 KB	Display	PDBx/mmCIF format
PDB format	pdb3zxb.ent.gz	90.2 KB	Display	PDB format
PDBx/mmJSON format	3zxb.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/zx/3zxb ftp://data.pdbj.org/pub/pdb/validation_reports/zx/3zxb	HTTPS FTP

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Related structure data

Related structure data	3zxcSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4a83-d 3so6-d 5aj8-2 4d70-2 7bx9-d 6z6i-3 2lt2-d 4s2v-d 6cwl-2 6ul3-1 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	#126 - Jun 2010 Epidermal Growth Factor similarity (1) #182 - Feb 2015 Insulin receptor similarity (1) #184 - Apr 2015 Glucagon similarity (1)

Deposited unit

A: SINGLE INSULIN-LIKE GROWTH FACTOR-BINDING DOMAIN PROTEIN-1

B: SINGLE INSULIN-LIKE GROWTH FACTOR-BINDING DOMAIN PROTEIN-1

C: SINGLE INSULIN-LIKE GROWTH FACTOR-BINDING DOMAIN PROTEIN-1

D: SINGLE INSULIN-LIKE GROWTH FACTOR-BINDING DOMAIN PROTEIN-1

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

1

A: SINGLE INSULIN-LIKE GROWTH FACTOR-BINDING DOMAIN PROTEIN-1

B: SINGLE INSULIN-LIKE GROWTH FACTOR-BINDING DOMAIN PROTEIN-1

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

2

C: SINGLE INSULIN-LIKE GROWTH FACTOR-BINDING DOMAIN PROTEIN-1

D: SINGLE INSULIN-LIKE GROWTH FACTOR-BINDING DOMAIN PROTEIN-1

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

Unit cell

Length a, b, c (Å)	62.247, 62.247, 169.297
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	SINGLE INSULIN-LIKE GROWTH FACTOR-BINDING DOMAIN PROTEIN-1 / SIBD-1 Mass: 8167.202 Da / Num. of mol.: 4 Fragment: INSULIN-LIKE GROWTH FACTOR BINDING DOMAIN, RESIDUES 20-97 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CUPIENNIUS SALEI (spider) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G4V4F9
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

SINGLE INSULIN-LIKE GROWTH FACTOR-BINDING DOMAIN PROTEIN-1 / SIBD-1

Mass: 8167.202 Da / Num. of mol.: 4
Fragment: INSULIN-LIKE GROWTH FACTOR BINDING DOMAIN, RESIDUES 20-97
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

CUPIENNIUS SALEI (spider) / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G4V4F9

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.94 Å³/Da / Density % sol: 58.23 % / Description: NONE
Crystal grow	pH: 8 Details: 1.4 M SODIUM CITRATE, 0.1 M TRIS, 2 % GLYCEROL, PH 8.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
Detector	Type: MARRESEARCH / Detector: CCD / Date: Jun 8, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection twin	Operator: -h,-k,l / Fraction: 0.495
Reflection	Resolution: 2.55→100 Å / Num. obs: 13082 / % possible obs: 99.7 % / Observed criterion σ(I): 2.96 / Redundancy: 7.7 % / R_merge(I) obs: 0.07 / Net I/σ(I): 23.9
Reflection shell	Resolution: 2.55→2.7 Å / Redundancy: 7.8 % / R_merge(I) obs: 0.1 / Mean I/σ(I) obs: 2.98 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZXC

3zxc

Resolution: 2.55→51.366 Å / σ(F): 1.99 / Phase error: 29.14 / Stereochemistry target values: TWIN_LSQ_F
Details: RESIDUES 59-69 IN CHAIN A, 60-69 IN CHAIN B, 61-69 IN CHAIN C, 59-69 IN CHAIN D ARE DISORDERED.

	R_factor	Num. reflection	% reflection
R_free	0.2504	653	5 %
R_work	0.2241	-	-
obs	0.2257	13035	99.78 %

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 85.545 Å² / k_sol: 0.354 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	15.3196 Å²	0 Å²	0 Å²
2-	-	15.3196 Å²	0 Å²
3-	-	-	-30.6393 Å²

Refinement step

Cycle: LAST / Resolution: 2.55→51.366 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1895	0	0	41	1936

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	1971
X-RAY DIFFRACTION	f_angle_d	1.425	2648
X-RAY DIFFRACTION	f_dihedral_angle_d	20.986	1206
X-RAY DIFFRACTION	f_chiral_restr	0.079	274
X-RAY DIFFRACTION	f_plane_restr	0.011	363

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 (%)
2.5505-2.8072	0.3063	160	0.3053	3033	X-RAY DIFFRACTION	95
2.8072-3.2133	0.3119	159	0.2774	3027	X-RAY DIFFRACTION	95
3.2133-4.0482	0.2469	162	0.2337	3079	X-RAY DIFFRACTION	95
4.0482-51.3767	0.2252	171	0.193	3232	X-RAY DIFFRACTION	94

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	0.5251	0.319	1.2116	-0.0475	0.3517	3.0698	-0.6763	-0.733	0.0301	0.5087	0.2572	-0.2491	-1.8177	-0.5467	0.3031	0.9301	0.2783	0.0739	0.6441	0.1333	0.5526	-23.5237	31.6321	27.786
2	5.5082	0.4543	-3.2587	2.3885	0.1497	2.018	0.666	0.8814	-0.3003	0.0037	-0.4093	-0.1011	-0.5137	-0.7384	-0.0526	0.529	-0.0264	-0.0111	0.6741	0.0216	0.4215	-24.2382	31.5899	37.1754
3	3.0258	2.2462	0.1684	6.8453	-1.6524	1.0066	0.5275	-1.3914	0.5104	-1.1281	-0.184	0.6966	0.5243	1.0739	-0.1782	0.3963	-0.073	-0.0573	0.5026	-0.1839	0.3726	-14.4867	28.1702	40.9723
4	7.0303	-0.7687	-0.4718	3.3951	-1.1044	2.5137	-0.5101	-0.5604	0.5498	-0.3526	0.9624	-0.144	0.4452	0.0084	-0.1858	0.4574	0.0126	-0.0813	0.4689	-0.0796	0.4337	-20.9943	31.8455	49.9004
5	2.2638	1.677	-0.3832	7.5967	3.5757	3.6555	0.2222	0.4418	1.2856	0.8584	-0.0379	0.7175	1.9537	1.3515	-0.0278	0.6685	0.2424	-0.0372	0.642	0.0311	0.4975	-13.3756	19.4939	45.3468
6	3.2512	0.6737	2.5692	6.277	-1.0655	6.5541	-1.2221	0.3184	-0.6735	-0.0417	0.5192	-1.1707	-0.7253	-0.6027	0.8106	1.1982	-0.0021	0.2227	0.2847	-0.1015	0.4017	-21.2965	16.4864	32.4742
7	4.4843	0.2728	-2.0771	1.2783	0.7136	5.9238	0.8656	1.2098	0.1207	-0.2693	-0.4774	0.0173	-0.836	0.4686	-0.693	0.7458	-0.1372	0.1194	0.6083	-0.0832	0.3512	-18.7178	20.0113	29.8487
8	0.8456	-0.631	0.3778	0.5047	0.168	1.0009	-0.0837	0.0432	0.3616	-0.1504	-0.2069	-0.4126	-0.5124	-0.3061	0.1349	0.2303	0.1033	0.1401	0.6482	0.0154	0.4175	-14.0795	22.8687	22.7632
9	5.4728	2.1956	1.415	3.0944	0.3678	9.7303	-1.0444	-0.4913	-0.1715	0.0507	0.2686	1.1189	-2.8035	-2.6921	0.4592	0.9342	0.3589	0.1084	1.144	0.1415	0.5019	-9.2058	53.0647	38.5494
10	0.9185	0.0694	-0.5121	2.5242	-0.4385	0.3014	-0.5848	0.6412	-0.092	0.0465	0.3052	0.1527	0.1361	-0.4226	0.1034	0.5448	-0.2981	-0.0474	0.653	0.0876	0.2988	-8.4109	45.2076	52.4811
11	1.7782	1.2164	-1.996	1.7046	-2.0122	2.5792	-0.5735	-0.4836	0.8223	-1.1613	0.4202	0.0599	0.2336	0.1179	-0.3074	0.8787	-0.0736	-0.0388	0.3809	-0.0218	0.433	-4.3563	51.4216	58.0464
12	4.955	2.0417	5.5352	4.9211	2.4783	8.584	0.1833	1.2495	0.7943	0.5402	0.1874	0.3985	1.4217	1.7131	-0.0205	0.47	-0.0367	0.1636	0.3353	-0.1247	0.0425	-2.3426	51.2981	67.1914
13	1.4928	-0.3684	-1.9693	1.1485	1.8452	4.8091	0.0322	-0.6239	0.2203	0.5964	-0.3408	-0.0417	0.9565	0.6585	0.019	0.8304	-0.1448	-0.0543	0.9799	-0.1342	0.6815	10.1019	49.8759	59.8726
14	4.5005	0.3482	-2.9818	0.2371	-0.3488	2.0466	-0.3515	2.2587	-0.46	-0.2903	0.5887	-0.6672	-0.2688	-1.7145	-0.0487	0.6602	-0.3111	0.1746	0.9459	-0.0175	0.8984	3.3508	37.1147	47.0102
15	7.8264	-0.8135	0.5813	8.2813	2.397	5.8527	-1.0338	-0.7649	1.4939	-0.4367	0.44	1.2093	0.261	0.9951	0.1644	0.4092	0.1646	-0.0853	0.4953	-0.2073	0.5733	8.7717	45.9468	50.1777
16	0.9282	-0.9129	-0.2489	2.1008	1.6405	1.7923	-0.2498	-0.4316	0.337	-0.1419	0.7918	-0.0991	0.2405	0.2481	-0.3794	0.8439	-0.1463	0.0222	0.4257	-0.0211	0.256	3.1504	50.2649	37.1699

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 1:18)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 19:38)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 39:48)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 49:78)
5	X-RAY DIFFRACTION	5	(CHAIN B AND RESID 1:13)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 14:26)
7	X-RAY DIFFRACTION	7	(CHAIN B AND RESID 27:39)
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESID 40:78)
9	X-RAY DIFFRACTION	9	(CHAIN C AND RESID 1:12)
10	X-RAY DIFFRACTION	10	(CHAIN C AND RESID 13:39)
11	X-RAY DIFFRACTION	11	(CHAIN C AND RESID 40:55)
12	X-RAY DIFFRACTION	12	(CHAIN C AND RESID 56:78)
13	X-RAY DIFFRACTION	13	(CHAIN D AND RESID 1:10)
14	X-RAY DIFFRACTION	14	(CHAIN D AND RESID 11:21)
15	X-RAY DIFFRACTION	15	(CHAIN D AND RESID 22:32)
16	X-RAY DIFFRACTION	16	(CHAIN D AND RESID 33:78)

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