PDB-7x44: Crystal structure of chlorotoxin mutant - Q11N

ID or keywords:

Entry

Database: PDB / ID: 7x44

Title

Crystal structure of chlorotoxin mutant - Q11N

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 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7x44.cif.gz	28.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7x44.ent.gz	15.5 KB	Display	PDB format
PDBx/mmJSON format	7x44.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7x44_validation.pdf.gz	412.1 KB	Display	wwPDB validaton report
Full document	7x44_full_validation.pdf.gz	412.1 KB	Display
Data in XML	7x44_validation.xml.gz	3.7 KB	Display
Data in CIF	7x44_validation.cif.gz	4.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x4/7x44 ftp://data.pdbj.org/pub/pdb/validation_reports/x4/7x44	HTTPS FTP

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Related structure data

Related structure data	7x41SC 7x43C 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

4.4 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)	22.420, 26.115, 47.421
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: 4398.170 Da / Num. of mol.: 1 / Mutation: Q11N 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.: 40 / 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: 22.06 %
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: 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: 13922 / % possible obs: 99.56 % / Redundancy: 5.4 % / R_merge(I) obs: 0.039 / Net I/σ(I): 48.9
Reflection shell	Resolution: 1.04→1.08 Å / R_merge(I) obs: 0.109 / Num. unique obs: 1355

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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→22.876 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.973 / SU B: 0.461 / SU ML: 0.011 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.022
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.13336	672	4.84 %
R_work	0.13113	13212	-
all	0.13124	-	-
obs	0.13124	13884	99.563 %

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: 6.655 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.017 Å²	-0 Å²	0 Å²
2-	-	-0.021 Å²	0 Å²
3-	-	-	0.004 Å²

Refinement step

Cycle: LAST / Resolution: 1.04→22.876 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	273	0	0	40	313

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	281
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.014	250
X-RAY DIFFRACTION	r_angle_refined_deg	1.471	1.686	375
X-RAY DIFFRACTION	r_angle_other_deg	1.53	1.617	583
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.46	5	36
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.361	19.286	14
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.631	15	51
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	8.562	15	3
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	34
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	322
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	64
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	56
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.184	0.2	225
X-RAY DIFFRACTION	r_nbtor_refined	0.165	0.2	131
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	141
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.143	0.2	18
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.061	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.153	0.2	10
X-RAY DIFFRACTION	r_nbd_other	0.172	0.2	39
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.029	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	0.333	0.382	147
X-RAY DIFFRACTION	r_mcbond_other	0.321	0.377	146
X-RAY DIFFRACTION	r_mcangle_it	0.482	0.573	182
X-RAY DIFFRACTION	r_mcangle_other	0.483	0.577	183
X-RAY DIFFRACTION	r_scbond_it	0.506	0.555	134
X-RAY DIFFRACTION	r_scbond_other	0.506	0.556	134
X-RAY DIFFRACTION	r_scangle_it	0.574	0.775	193
X-RAY DIFFRACTION	r_scangle_other	0.571	0.775	193
X-RAY DIFFRACTION	r_lrange_it	1.339	5.717	308
X-RAY DIFFRACTION	r_lrange_other	1.209	5.291	301
X-RAY DIFFRACTION	r_rigid_bond_restr	0.781	3	531

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	0.134	51	0.128	936	0.128	1004	0.978	0.981	98.3068	0.104
1.067-1.096	0.185	41	0.105	936	0.107	977	0.969	0.985	100	0.088
1.096-1.128	0.112	48	0.098	917	0.099	966	0.984	0.986	99.8965	0.082
1.128-1.163	0.105	40	0.095	880	0.095	921	0.987	0.988	99.8914	0.083
1.163-1.201	0.095	43	0.097	861	0.097	904	0.99	0.988	100	0.087
1.201-1.243	0.095	48	0.097	840	0.097	888	0.989	0.988	100	0.089
1.243-1.289	0.127	45	0.102	786	0.103	831	0.98	0.986	100	0.095
1.289-1.342	0.139	49	0.105	759	0.107	808	0.978	0.986	100	0.1
1.342-1.401	0.114	33	0.106	768	0.107	801	0.983	0.986	100	0.102
1.401-1.469	0.12	40	0.102	710	0.103	750	0.983	0.987	100	0.103
1.469-1.549	0.114	42	0.113	681	0.113	724	0.985	0.984	99.8619	0.115
1.549-1.642	0.124	32	0.117	653	0.117	688	0.984	0.982	99.564	0.123
1.642-1.755	0.147	29	0.124	606	0.125	636	0.975	0.981	99.8428	0.133
1.755-1.894	0.103	27	0.132	581	0.131	608	0.989	0.982	100	0.146
1.894-2.074	0.14	19	0.144	533	0.143	556	0.984	0.98	99.2806	0.17
2.074-2.316	0.154	24	0.155	476	0.155	503	0.975	0.976	99.4036	0.185
2.316-2.67	0.167	15	0.166	448	0.166	463	0.962	0.963	100	0.204
2.67-3.259	0.163	17	0.167	383	0.167	400	0.968	0.964	100	0.206
3.259-4.563	0.153	24	0.158	275	0.157	311	0.978	0.972	96.1415	0.205
4.563-22.876	0.227	5	0.258	183	0.257	202	0.905	0.947	93.0693	0.358

Refinement TLS params.

Method: refined / Origin x: -3.6506 Å / Origin y: 4.0621 Å / Origin z: -6.7499 Å

	11	12	13	21	22	23	31	32	33
T	0.0057 Å²	-0.001 Å²	0.0008 Å²	-	0.0122 Å²	-0.0024 Å²	-	-	0.0128 Å²
L	0.8981 °²	0.1776 °²	0.2265 °²	-	0.0602 °²	0.0678 °²	-	-	0.7354 °²
S	-0.0008 Å °	-0.0001 Å °	0.011 Å °	0.0037 Å °	-0.0142 Å °	0.0146 Å °	-0.0165 Å °	0.0002 Å °	0.015 Å °

Refinement TLS group

Selection: ALL

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