PDB-9vvn: Crystal structure of computationally designed protein VTP-4

ID or keywords:

Entry

Database: PDB / ID: 9vvn

Title

Crystal structure of computationally designed protein VTP-4

Components

VTP-4

Keywords

DE NOVO PROTEIN / Verteporfin binding

Function / homology

2,5,8,11,14,17-HEXAOXANONADECAN-19-OL

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Tang, X. / Li, Y.H. / Xu, Y.L. / Kou, L.Y. / Ji, P.F.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Computational design of verteporfin binding protein
Authors: Tang, X. / Li, Y.H. / Xu, Y.L. / Kou, L.Y. / Ji, P.F.

History

Deposition	Jul 16, 2025	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Aug 13, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9vvn.cif.gz	54.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9vvn.ent.gz	35.5 KB	Display	PDB format
PDBx/mmJSON format	9vvn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9vvn_validation.pdf.gz	628.7 KB	Display	wwPDB validaton report
Full document	9vvn_full_validation.pdf.gz	630.9 KB	Display
Data in XML	9vvn_validation.xml.gz	12 KB	Display
Data in CIF	9vvn_validation.cif.gz	16.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vv/9vvn ftp://data.pdbj.org/pub/pdb/validation_reports/vv/9vvn	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: VTP-4

hetero molecules

20.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	35.606, 58.488, 83.828
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	VTP-4 Mass: 20361.348 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-P15 / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL Mass: 296.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₃H₂₈O₇
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.14 Å³/Da / Density % sol: 42.62 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.01M NiCl2, 0.1M Tris-HCl pH8.5, 20% w/v Polyethylene glycol Monomethyl ether 2,000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 0.99999 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 12, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99999 Å / Relative weight: 1
Reflection	Resolution: 1.6→47.97 Å / Num. obs: 23836 / % possible obs: 99.9 % / Redundancy: 11 % / R_merge(I) obs: 0.085 / Net I/σ(I): 14.9
Reflection shell	Resolution: 1.6→1.63 Å / R_merge(I) obs: 0.996 / Num. unique obs: 1157

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.6→47.967 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.928 / SU B: 2.061 / SU ML: 0.073 / Cross valid method: FREE R-VALUE / ESU R: 0.102 / ESU R Free: 0.107
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2546	1169	4.916 %
R_work	0.2073	22612	-
all	0.21	-	-
obs	-	23781	99.828 %

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: 24.626 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.008 Å²	-0 Å²	-0 Å²
2-	-	-0.218 Å²	0 Å²
3-	-	-	0.21 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→47.967 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1308	0	28	135	1471

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	1409
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1417
X-RAY DIFFRACTION	r_angle_refined_deg	2.003	1.835	1915
X-RAY DIFFRACTION	r_angle_other_deg	0.625	1.727	3275
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.13	5	182
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.773	5	5
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.28	10	237
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.136	10	58
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	222
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	1591
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	305
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	264
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.201	0.2	1221
X-RAY DIFFRACTION	r_nbtor_refined	0.191	0.2	673
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.089	0.2	736
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.2	0.2	89
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.084	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.218	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.19	0.2	55
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.265	0.2	17
X-RAY DIFFRACTION	r_mcbond_it	2.527	2.298	683
X-RAY DIFFRACTION	r_mcbond_other	2.527	2.297	683
X-RAY DIFFRACTION	r_mcangle_it	3.486	4.125	856
X-RAY DIFFRACTION	r_mcangle_other	3.49	4.127	857
X-RAY DIFFRACTION	r_scbond_it	3.795	2.828	726
X-RAY DIFFRACTION	r_scbond_other	3.792	2.828	727
X-RAY DIFFRACTION	r_scangle_it	5.814	4.947	1051
X-RAY DIFFRACTION	r_scangle_other	5.811	4.947	1052
X-RAY DIFFRACTION	r_lrange_it	7.495	30.844	1588
X-RAY DIFFRACTION	r_lrange_other	7.438	27.903	1552

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
1.6-1.642	0.359	86	0.281	1625	0.284	1729	0.923	0.951	98.9589	0.26
1.642-1.686	0.354	87	0.271	1604	0.275	1692	0.925	0.956	99.9409	0.248
1.686-1.735	0.308	84	0.254	1528	0.257	1622	0.95	0.962	99.3835	0.228
1.735-1.789	0.255	64	0.224	1535	0.225	1607	0.962	0.969	99.5022	0.201
1.789-1.847	0.271	75	0.225	1472	0.227	1547	0.951	0.967	100	0.202
1.847-1.912	0.229	79	0.225	1412	0.225	1493	0.963	0.968	99.866	0.206
1.912-1.984	0.283	86	0.228	1353	0.232	1440	0.953	0.967	99.9306	0.21
1.984-2.065	0.286	72	0.227	1331	0.23	1403	0.95	0.969	100	0.215
2.065-2.156	0.241	68	0.23	1281	0.231	1349	0.969	0.968	100	0.219
2.156-2.261	0.26	69	0.207	1224	0.209	1293	0.96	0.973	100	0.197
2.261-2.384	0.244	53	0.194	1180	0.196	1233	0.965	0.976	100	0.187
2.384-2.528	0.298	56	0.205	1107	0.209	1163	0.939	0.974	100	0.204
2.528-2.702	0.222	45	0.208	1057	0.209	1102	0.965	0.972	100	0.21
2.702-2.917	0.3	44	0.203	983	0.206	1027	0.94	0.973	100	0.206
2.917-3.195	0.242	41	0.2	912	0.202	953	0.967	0.974	100	0.209
3.195-3.57	0.183	53	0.172	812	0.172	865	0.978	0.982	100	0.187
3.57-4.118	0.181	37	0.183	734	0.183	771	0.979	0.978	100	0.205
4.118-5.035	0.341	26	0.169	645	0.174	671	0.926	0.982	100	0.204
5.035-7.081	0.268	26	0.242	508	0.243	534	0.966	0.963	100	0.273
7.081-47.967	0.276	18	0.232	309	0.235	328	0.96	0.959	99.6951	0.264

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