PDB-7x41: Crystal structure of chlorotoxin, a glioma specific scorpion toxin

ID or keywords:

Entry

Database: PDB / ID: 7x41

Title

Crystal structure of chlorotoxin, a glioma specific scorpion toxin

Components

Chlorotoxin

Keywords

TOXIN / Neurotoxin / Anti-glioma migration agent / Glioma diagnosis

Function / homology

Scorpion short chain toxin, chloride channel inhibitor / Scorpion short toxin / Scorpion short toxin chloride channel inhibitor subfamily profile. / peptidase inhibitor activity / Knottin, scorpion toxin-like superfamily / chloride channel regulator activity / toxin activity / extracellular region / Chlorotoxin

Function and homology information

Biological species

Leiurus quinquestriatus quinquestriatus (Egyptian scorpion)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.15 Å

Authors

Chang, Y.T. / Chuang, W.J.

Funding support

Taiwan, 1items

Citation

Journal: To Be Published
Title: Expression in Pichia pastoris and characterization of chlorotoxin, an anti-glioma migration agent
Authors: Chang, Y.T.

History

Deposition	Mar 1, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 8, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7x41.cif.gz	27.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7x41.ent.gz	15.3 KB	Display	PDB format
PDBx/mmJSON format	7x41.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7x41_validation.pdf.gz	412.6 KB	Display	wwPDB validaton report
Full document	7x41_full_validation.pdf.gz	412.6 KB	Display
Data in XML	7x41_validation.xml.gz	3.6 KB	Display
Data in CIF	7x41_validation.cif.gz	4.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x4/7x41 ftp://data.pdbj.org/pub/pdb/validation_reports/x4/7x41	HTTPS FTP

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Related structure data

Related structure data	7x43C 7x44C 7x4dC 1chlS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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	#199 - Jul 2016 Monellin similarity (1) #38 - Feb 2003 Potassium Channels similarity (1)

Deposited unit

A: Chlorotoxin

4.41 kDa, 1 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)	22.335, 26.008, 47.230
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein/peptide	Chlorotoxin / CTX / ClTx Mass: 4412.196 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leiurus quinquestriatus quinquestriatus (Egyptian scorpion) Production host: Pichia (fungus) / References: UniProt: P45639
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 34 / 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: 1.55 Å³/Da / Density % sol: 20.88 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1 M monosodium phosphate and 0.75 M sodium citrate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97622 Å / Relative weight: 1
Reflection	Resolution: 1.15→30 Å / Num. obs: 10293 / % possible obs: 99.7 % / Redundancy: 5.5 % / R_merge(I) obs: 0.04 / Net I/σ(I): 51.1
Reflection shell	Resolution: 1.15→1.19 Å / R_merge(I) obs: 0.09 / Num. unique obs: 1010

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
HKL-2000	2.3.10	data reduction
HKL-2000	2.3.10	data scaling
HKL-3000	2.3.10	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1CHL

1chl

Resolution: 1.15→23.615 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.95 / SU B: 0.688 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.033
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1574	511	4.984 %
R_work	0.1445	9742	-
all	0.145	-	-
obs	-	10253	99.66 %

Solvent computation

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

Displacement parameters

B_iso mean: 6.327 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.086 Å²	0 Å²	0 Å²
2-	-	0.082 Å²	-0 Å²
3-	-	-	-0.168 Å²

Refinement step

Cycle: LAST / Resolution: 1.15→23.615 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	274	0	0	34	308

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	282
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.014	252
X-RAY DIFFRACTION	r_angle_refined_deg	1.451	1.687	376
X-RAY DIFFRACTION	r_angle_other_deg	1.528	1.616	588
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.359	5	36
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.437	19.286	14
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.325	15	52
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	5.777	15	3
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	34
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	322
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	64
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	53
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.188	0.2	232
X-RAY DIFFRACTION	r_nbtor_refined	0.166	0.2	131
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	146
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.095	0.2	15
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.176	0.2	7
X-RAY DIFFRACTION	r_nbd_other	0.161	0.2	35
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.078	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	0.293	0.325	147
X-RAY DIFFRACTION	r_mcbond_other	0.273	0.318	146
X-RAY DIFFRACTION	r_mcangle_it	0.397	0.483	182
X-RAY DIFFRACTION	r_mcangle_other	0.396	0.489	183
X-RAY DIFFRACTION	r_scbond_it	0.561	0.533	135
X-RAY DIFFRACTION	r_scbond_other	0.545	0.537	135
X-RAY DIFFRACTION	r_scangle_it	0.662	0.73	194
X-RAY DIFFRACTION	r_scangle_other	0.662	0.733	194
X-RAY DIFFRACTION	r_lrange_it	1.01	4.662	302
X-RAY DIFFRACTION	r_lrange_other	0.909	4.443	298
X-RAY DIFFRACTION	r_rigid_bond_restr	0.87	3	534

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.15-1.18	0.157	36	0.105	715	0.107	755	0.981	0.987	99.4702	0.09
1.18-1.212	0.115	39	0.102	672	0.103	711	0.984	0.985	100	0.087
1.212-1.247	0.121	50	0.102	666	0.103	716	0.983	0.986	100	0.09
1.247-1.285	0.156	39	0.107	633	0.109	672	0.975	0.984	100	0.097
1.285-1.327	0.14	44	0.107	625	0.109	670	0.979	0.984	99.8507	0.099
1.327-1.374	0.115	36	0.113	608	0.113	644	0.982	0.984	100	0.106
1.374-1.425	0.137	28	0.113	593	0.114	622	0.981	0.983	99.8392	0.107
1.425-1.483	0.12	31	0.105	574	0.106	605	0.985	0.984	100	0.102
1.483-1.549	0.125	17	0.12	546	0.12	564	0.981	0.98	99.8227	0.122
1.549-1.624	0.126	31	0.119	537	0.12	569	0.979	0.98	99.8243	0.122
1.624-1.712	0.114	19	0.135	516	0.134	535	0.981	0.974	100	0.141
1.712-1.815	0.223	18	0.144	467	0.147	485	0.95	0.972	100	0.154
1.815-1.94	0.16	29	0.148	453	0.149	483	0.948	0.967	99.793	0.16
1.94-2.094	0.154	20	0.159	418	0.159	440	0.974	0.966	99.5455	0.183
2.094-2.292	0.219	19	0.178	394	0.18	414	0.941	0.962	99.7585	0.201
2.292-2.559	0.156	19	0.165	355	0.164	375	0.978	0.966	99.7333	0.194
2.559-2.95	0.247	8	0.173	332	0.174	340	0.957	0.966	100	0.218
2.95-3.598	0.213	11	0.182	284	0.183	296	0.963	0.97	99.6622	0.24
3.598-5.031	0.153	7	0.194	221	0.192	234	0.979	0.965	97.4359	0.259
5.031-23.615	0.259	10	0.288	132	0.286	153	0.963	0.916	92.8105	0.369

Refinement TLS params.

Method: refined / Origin x: -3.6063 Å / Origin y: 3.9806 Å / Origin z: -6.677 Å

	11	12	13	21	22	23	31	32	33
T	0.0011 Å²	0 Å²	-0.0004 Å²	-	0.0129 Å²	0.0007 Å²	-	-	0.0201 Å²
L	0.9429 °²	0.1316 °²	0.211 °²	-	0.0465 °²	0.0183 °²	-	-	0.6717 °²
S	0.003 Å °	0.0018 Å °	0.0071 Å °	0.0008 Å °	-0.0124 Å °	0.016 Å °	-0.0254 Å °	0.0058 Å °	0.0094 Å °

Refinement TLS group

Selection: ALL

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