PDB-26qz: Crystal structure of Rhodostomin ARGDP mutant

ID or keywords:

Entry

Database: PDB / ID: 26qz

Title

Crystal structure of Rhodostomin ARGDP mutant

Components

Disintegrin rhodostomin

Keywords

BLOOD CLOTTING / Disintegrin / Platelet aggregation inhibitor

Function / homology

Function and homology information

Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / toxin activity / proteolysis / extracellular region / metal ion binding / plasma membrane
Similarity search - Function

Biological species

Calloselasma rhodostoma (Malayan pit viper)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.804 Å

Authors

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

Funding support

Taiwan, 1items

Citation

Journal: To Be Published
Title: Crystal structure of Rhodostomin ARGDP mutant
Authors: Chang, Y.T. / Chuang, W.J.

History

Deposition	May 11, 2026	Deposition site: PDBJ / Processing site: PDBJ
Supersession	May 27, 2026	ID: 4M4C
Revision 1.0	May 27, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	26qz.cif.gz	107 KB	Display	PDBx/mmCIF format
PDB format	pdb26qz.ent.gz	79.9 KB	Display	PDB format
PDBx/mmJSON format	26qz.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/6q/26qz ftp://data.pdbj.org/pub/pdb/validation_reports/6q/26qz	HTTPS FTP

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Related structure data

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	#28 - Apr 2002 Anthrax Toxin similarity (1) #237 - Sep 2019 Nanodiscs and HDL similarity (1) #44 - Aug 2003 Calmodulin similarity (1)

Deposited unit

A: Disintegrin rhodostomin

B: Disintegrin rhodostomin

C: Disintegrin rhodostomin

D: Disintegrin rhodostomin

hetero molecules

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

1

A: Disintegrin rhodostomin

defined by author&software
Evidence: mass spectrometry
7.28 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Disintegrin rhodostomin

hetero molecules

defined by author&software
7.47 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Disintegrin rhodostomin

hetero molecules

defined by author&software
7.47 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Disintegrin rhodostomin

hetero molecules

defined by author&software
7.47 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	31.619, 42.637, 46.538
Angle α, β, γ (deg.)	106.839, 103.858, 97.232
Int Tables number	1
Space group name H-M	P1

#1: Protein	Disintegrin rhodostomin / RHO / RHOD / Disintegrin kistrin / Platelet aggregation activation inhibitor Mass: 7281.243 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Calloselasma rhodostoma (Malayan pit viper) Production host: Komagataella pastoris (fungus) / References: UniProt: P30403
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 1.96 Å³/Da / Density % sol: 37.15 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% PEG4000, 0.2M Ammonium sulfate, 5% PEG3350, 2% PEG200, 0.5% 2-propanol(External) , pH 8.0

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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 210 / Detector: CCD / Date: Sep 16, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97622 Å / Relative weight: 1
Reflection	Resolution: 1.8→30 Å / Num. obs: 19633 / % possible obs: 96.7 % / Redundancy: 3.7 % / R_merge(I) obs: 0.059 / Net I/σ(I): 23.9
Reflection shell	Resolution: 1.8→1.86 Å / R_merge(I) obs: 0.459 / Num. unique obs: 1886

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.804→23.581 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.931 / SU B: 7.351 / SU ML: 0.1 / Cross valid method: FREE R-VALUE / ESU R: 0.44 / ESU R Free: 0.141
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2332	961	4.895 %
R_work	0.157	18670	-
all	0.161	-	-
obs	-	19631	96.481 %

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: 35.167 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.327 Å²	0.031 Å²	1.39 Å²
2-	-	-1.102 Å²	-0.61 Å²
3-	-	-	-0.4 Å²

Refinement step

Cycle: LAST / Resolution: 1.804→23.581 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1893	0	30	50	1973

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	1976
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.013	1699
X-RAY DIFFRACTION	r_angle_refined_deg	1.476	1.674	2677
X-RAY DIFFRACTION	r_angle_other_deg	1.316	1.604	3984
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.196	5	258
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.818	20.708	113
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.621	15	316
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.739	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	253
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	2265
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	423
X-RAY DIFFRACTION	r_nbd_refined	0.193	0.2	366
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.2	0.2	1608
X-RAY DIFFRACTION	r_nbtor_refined	0.152	0.2	938
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	950
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.155	0.2	69
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.016	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.277	0.2	43
X-RAY DIFFRACTION	r_nbd_other	0.219	0.2	161
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.187	0.2	20
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.162	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	3.984	2.883	1038
X-RAY DIFFRACTION	r_mcbond_other	3.98	2.88	1037
X-RAY DIFFRACTION	r_mcangle_it	4.741	4.317	1291
X-RAY DIFFRACTION	r_mcangle_other	4.743	4.321	1292
X-RAY DIFFRACTION	r_scbond_it	5.635	3.713	938
X-RAY DIFFRACTION	r_scbond_other	5.239	3.621	915
X-RAY DIFFRACTION	r_scangle_it	6.767	5.336	1385
X-RAY DIFFRACTION	r_scangle_other	6.307	5.192	1350
X-RAY DIFFRACTION	r_lrange_it	6.298	35.736	1975
X-RAY DIFFRACTION	r_lrange_other	6.303	35.714	1974
X-RAY DIFFRACTION	r_rigid_bond_restr	2.606	3	3675

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
1.804-1.851	0.282	79	0.199	1282	0.204	1541	0.846	0.856	88.3193	0.171
1.851-1.901	0.255	75	0.195	1270	0.199	1432	0.859	0.871	93.9246	0.162
1.901-1.956	0.256	64	0.167	1314	0.171	1429	0.883	0.904	96.4311	0.133
1.956-2.016	0.237	55	0.145	1275	0.149	1371	0.908	0.926	97.0095	0.117
2.016-2.082	0.22	45	0.131	1230	0.134	1322	0.921	0.946	96.4448	0.105
2.082-2.154	0.206	55	0.128	1211	0.131	1310	0.937	0.951	96.6412	0.109
2.154-2.235	0.178	57	0.112	1155	0.115	1256	0.948	0.965	96.4968	0.095
2.235-2.325	0.21	58	0.13	1079	0.134	1174	0.93	0.953	96.8484	0.114
2.325-2.427	0.228	66	0.136	1061	0.142	1156	0.931	0.947	97.4913	0.121
2.427-2.544	0.224	48	0.131	1026	0.135	1102	0.933	0.956	97.4592	0.12
2.544-2.68	0.229	47	0.145	982	0.15	1055	0.94	0.947	97.5355	0.137
2.68-2.841	0.229	48	0.188	919	0.19	982	0.92	0.919	98.4725	0.18
2.841-3.034	0.262	52	0.168	850	0.174	918	0.91	0.936	98.2571	0.171
3.034-3.272	0.309	44	0.165	841	0.171	902	0.874	0.939	98.1153	0.176
3.272-3.578	0.229	37	0.154	740	0.157	792	0.932	0.956	98.1061	0.175
3.578-3.988	0.17	28	0.129	679	0.131	717	0.956	0.974	98.6053	0.147
3.988-4.584	0.214	39	0.164	600	0.167	648	0.942	0.955	98.6111	0.196
4.584-5.561	0.213	25	0.173	507	0.175	537	0.945	0.956	99.0689	0.218
5.561-7.655	0.307	21	0.193	412	0.198	436	0.918	0.946	99.3119	0.25
7.655-23.581	0.267	18	0.24	237	0.242	256	0.893	0.926	99.6094	0.3

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	0.683	-0.4833	-0.577	0.7097	1.0581	1.6702	-0.063	0.0956	0.0805	0.0887	-0.0455	0.0254	0.1501	-0.0631	0.1085	0.0239	-0.0172	0.0189	0.024	0.0004	0.0527	-7.0409	20.1716	-24.1247
2	0.5752	-0.4617	-0.7171	0.4191	0.8071	2.0219	0.0104	-0.0533	-0.0171	-0.0019	0.0322	-0.0024	0.0466	0.0313	-0.0426	0.0327	0.0032	0.0069	0.0141	0.0139	0.0176	-13.9454	-1.4887	-32.8872
3	0.9317	0.4365	-0.8461	0.4049	0.0999	2.0448	-0.0389	0.0565	0.0649	-0.0119	0.0167	0.06	0.0067	-0.0849	0.0221	0.0468	0.0146	-0.0016	0.0175	0.012	0.0215	-2.0388	-4.9976	-12.1366
4	1.1287	0.2703	-0.6937	0.7696	0.0505	0.4974	0.0203	0.0379	0.0234	-0.0088	0.0129	-0.0105	-0.0214	-0.0189	-0.0332	0.0222	-0.0037	0.005	0.0173	-0.0008	0.0319	0.529	9.3959	-3.5517

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	3 - 67
2	X-RAY DIFFRACTION	2	ALL	B	3 - 67
3	X-RAY DIFFRACTION	3	ALL	C	3 - 67
4	X-RAY DIFFRACTION	4	ALL	D	4 - 68

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