PDB-7x43: Crystal structure of chlorotoxin mutant - M1R

ID or keywords:

Entry

Database: PDB / ID: 7x43

Title

Crystal structure of chlorotoxin mutant - M1R

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: 1.04 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
Revision 1.2	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7x43.cif.gz	28.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7x43.ent.gz	15.7 KB	Display	PDB format
PDBx/mmJSON format	7x43.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7x43_validation.pdf.gz	412.1 KB	Display	wwPDB validaton report
Full document	7x43_full_validation.pdf.gz	412 KB	Display
Data in XML	7x43_validation.xml.gz	3.7 KB	Display
Data in CIF	7x43_validation.cif.gz	4.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x4/7x43 ftp://data.pdbj.org/pub/pdb/validation_reports/x4/7x43	HTTPS FTP

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Related structure data

Related structure data	7x41SC 7x44C 7x4dC 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

4.44 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)	22.390, 26.500, 47.257
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: 4438.194 Da / Num. of mol.: 1 / Mutation: M1R 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.: 41 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.58 Å³/Da / Density % sol: 22.12 %
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: BL13B1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 15, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.04→30 Å / Num. obs: 14128 / % possible obs: 99.92 % / Redundancy: 6.5 % / R_merge(I) obs: 0.036 / Net I/σ(I): 45.5
Reflection shell	Resolution: 1.04→1.08 Å / R_merge(I) obs: 0.164 / Num. unique obs: 1379

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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: 7X41

7x41

Resolution: 1.04→23.628 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.962 / SU B: 0.506 / SU ML: 0.012 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.024
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1457	711	5.048 %
R_work	0.1393	13375	-
all	0.14	-	-
obs	-	14086	99.922 %

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: 7.418 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.013 Å²	-0 Å²	0 Å²
2-	-	0.029 Å²	0 Å²
3-	-	-	-0.042 Å²

Refinement step

Cycle: LAST / Resolution: 1.04→23.628 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	276	0	0	41	317

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	284
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.013	256
X-RAY DIFFRACTION	r_angle_refined_deg	1.468	1.686	378
X-RAY DIFFRACTION	r_angle_other_deg	1.528	1.621	595
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.248	5	36
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.688	18.125	16
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.686	15	52
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.495	15	4
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	34
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	319
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	69
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	56
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.183	0.2	236
X-RAY DIFFRACTION	r_nbtor_refined	0.165	0.2	131
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	148
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.132	0.2	30
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.25	0.2	7
X-RAY DIFFRACTION	r_nbd_other	0.169	0.2	38
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.053	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	0.418	0.434	147
X-RAY DIFFRACTION	r_mcbond_other	0.391	0.428	146
X-RAY DIFFRACTION	r_mcangle_it	0.622	0.651	182
X-RAY DIFFRACTION	r_mcangle_other	0.629	0.657	183
X-RAY DIFFRACTION	r_scbond_it	0.668	0.673	137
X-RAY DIFFRACTION	r_scbond_other	0.666	0.684	138
X-RAY DIFFRACTION	r_scangle_it	0.8	0.925	196
X-RAY DIFFRACTION	r_scangle_other	0.798	0.937	197
X-RAY DIFFRACTION	r_lrange_it	1.502	6.834	325
X-RAY DIFFRACTION	r_lrange_other	1.288	6.084	314
X-RAY DIFFRACTION	r_rigid_bond_restr	0.853	3	540

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
1.04-1.067	0.16	53	0.153	987	0.153	1041	0.97	0.977	99.9039	0.119
1.067-1.096	0.095	51	0.117	918	0.116	969	0.983	0.983	100	0.091
1.096-1.128	0.117	44	0.102	947	0.103	991	0.985	0.986	100	0.081
1.128-1.162	0.128	38	0.104	898	0.105	936	0.982	0.985	100	0.087
1.162-1.2	0.11	42	0.103	861	0.103	903	0.986	0.986	100	0.089
1.2-1.243	0.1	51	0.103	843	0.103	894	0.986	0.987	100	0.088
1.243-1.289	0.125	46	0.105	795	0.106	841	0.981	0.985	100	0.093
1.289-1.342	0.152	40	0.108	786	0.11	826	0.974	0.982	100	0.098
1.342-1.401	0.149	50	0.109	759	0.112	809	0.977	0.983	100	0.098
1.401-1.469	0.096	44	0.113	703	0.112	747	0.986	0.983	100	0.107
1.469-1.549	0.113	37	0.114	689	0.114	726	0.984	0.983	100	0.11
1.549-1.642	0.116	39	0.115	649	0.115	689	0.983	0.983	99.8549	0.112
1.642-1.755	0.15	36	0.128	613	0.129	650	0.979	0.981	99.8462	0.132
1.755-1.894	0.13	25	0.146	587	0.145	612	0.976	0.977	100	0.152
1.894-2.074	0.153	26	0.154	540	0.154	567	0.973	0.974	99.8236	0.17
2.074-2.317	0.17	23	0.168	488	0.168	511	0.967	0.968	100	0.194
2.317-2.671	0.183	22	0.168	442	0.169	464	0.948	0.966	100	0.199
2.671-3.26	0.203	18	0.174	382	0.175	400	0.963	0.968	100	0.211
3.26-4.568	0.193	15	0.157	300	0.158	318	0.962	0.978	99.0566	0.202
4.568-23.628	0.211	11	0.29	187	0.285	202	0.958	0.942	98.0198	0.409

Refinement TLS params.

Method: refined / Origin x: 3.7746 Å / Origin y: -4.1429 Å / Origin z: -6.8749 Å

	11	12	13	21	22	23	31	32	33
T	0.003 Å²	0.0032 Å²	0.0031 Å²	-	0.0094 Å²	0.0029 Å²	-	-	0.0122 Å²
L	0.661 °²	0.1514 °²	-0.1286 °²	-	0.0589 °²	0.0261 °²	-	-	0.6593 °²
S	0.0121 Å °	-0.0127 Å °	-0.0052 Å °	-0.0009 Å °	-0.014 Å °	-0.0135 Å °	0.0223 Å °	-0.003 Å °	0.0019 Å °

Refinement TLS group

Selection: ALL

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