PDB-6lov: crystal structure of alpha-momorcharin in complex with xanthosine

ID or keywords:

Entry

Database: PDB / ID: 6lov

Title

crystal structure of alpha-momorcharin in complex with xanthosine

Components

Ribosome-inactivating protein momordin I

Keywords

PLANT PROTEIN / alpha-momorcharin / ribosome-inactivating protein / rRNA N-glycosidase / xanthosine

Function / homology

Function and homology information

rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / negative regulation of translation
Similarity search - Function

Biological species

Momordica charantia (bitter melon)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.35 Å

Authors

Fan, X. / Jin, T.

Citation

Journal: Int.J.Biol.Macromol. / Year: 2020
Title: Atomic-resolution structures of type I ribosome inactivating protein alpha-momorcharin with different substrate analogs.
Authors: Fan, X. / Wang, Y. / Guo, F. / Zhang, Y. / Jin, T.

History

Deposition	Jan 7, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 18, 2020	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6lov.cif.gz	108.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6lov.ent.gz	78.8 KB	Display	PDB format
PDBx/mmJSON format	6lov.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6lov_validation.pdf.gz	865.2 KB	Display	wwPDB validaton report
Full document	6lov_full_validation.pdf.gz	868.5 KB	Display
Data in XML	6lov_validation.xml.gz	13.7 KB	Display
Data in CIF	6lov_validation.cif.gz	19.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lo/6lov ftp://data.pdbj.org/pub/pdb/validation_reports/lo/6lov	HTTPS FTP

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Related structure data

Related structure data	6loqC 6lorC 6lowC 6loyC 6lozC 6lp0C 1f8qS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6z1y-4 1ahc-d 4dwm-d 3ej5-d 2jdl-1 5ilx-d 3s9q-d 3hiq-1 6z1y-2 1giu-d 4lt4-d 5gu4-1 3v2k-d 2wk0-2 Search similar-shape structures by Omokage search (details) 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	#161 - May 2013 Ricin similarity (9) #69 - Sep 2005 Cholera Toxin similarity (9)

Deposited unit

A: Ribosome-inactivating protein momordin I

hetero molecules

31.8 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)	130.530, 130.530, 39.737
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	146
Space group name H-M	H3

#1: Protein	Ribosome-inactivating protein momordin I / Alpha-momorcharin / Alpha-MMC / rRNA N-glycosidase Mass: 31562.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Momordica charantia (bitter melon) / References: UniProt: P16094, rRNA N-glycosylase
#2: Chemical	ChemComp-4UO / 2,3-dihydroxanthosine / Xanthosine Mass: 284.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₂N₄O₆ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.06 Å³/Da / Density % sol: 40.41 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M Magnesium Acetate, 20% PEG 8000, 0.1 M Sodium cacodylate, pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2007
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.349→50 Å / Num. obs: 52296 / % possible obs: 94.1 % / Redundancy: 3.2 % / CC_1/2: 0.987 / R_merge(I) obs: 0.077 / Net I/σ(I): 8.9
Reflection shell	Resolution: 1.35→1.4 Å / R_merge(I) obs: 0.745 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5551 / CC_1/2: 0.658

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1F8Q

1f8q

Resolution: 1.35→18.847 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.937 / SU B: 3.384 / SU ML: 0.064 / Cross valid method: FREE R-VALUE / ESU R: 0.074 / ESU R Free: 0.075
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2585	2608	4.987 %
R_work	0.2308	-	-
all	0.232	-	-
obs	-	52296	93.971 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 26.356 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.817 Å²	-0.409 Å²	0 Å²
2-	-	-0.817 Å²	0 Å²
3-	-	-	2.651 Å²

Refinement step

Cycle: LAST / Resolution: 1.35→18.847 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1916	0	20	206	2142

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	1988
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	1869
X-RAY DIFFRACTION	r_angle_refined_deg	1.703	1.661	2707
X-RAY DIFFRACTION	r_angle_other_deg	1.421	1.576	4322
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.924	5	247
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.648	21.359	103
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.099	15	333
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.44	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	270
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	2221
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	426
X-RAY DIFFRACTION	r_nbd_refined	0.206	0.2	435
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.182	0.2	1821
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	989
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	881
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.138	0.2	145
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.333	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.241	0.2	49
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.233	0.2	17
X-RAY DIFFRACTION	r_mcbond_it	1.099	1.956	985
X-RAY DIFFRACTION	r_mcbond_other	1.097	1.954	984
X-RAY DIFFRACTION	r_mcangle_it	1.68	2.931	1233
X-RAY DIFFRACTION	r_mcangle_other	1.68	2.933	1234
X-RAY DIFFRACTION	r_scbond_it	1.624	2.208	1003
X-RAY DIFFRACTION	r_scbond_other	1.624	2.21	1004
X-RAY DIFFRACTION	r_scangle_it	2.489	3.242	1474
X-RAY DIFFRACTION	r_scangle_other	2.488	3.244	1475
X-RAY DIFFRACTION	r_lrange_it	5.278	24.951	2332
X-RAY DIFFRACTION	r_lrange_other	4.953	24.271	2287

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.35-1.384	0.361	213	0.34	3830	X-RAY DIFFRACTION	97.8461
1.384-1.422	0.339	233	0.314	3787	X-RAY DIFFRACTION	99.9006
1.422-1.463	0.255	179		3692	X-RAY DIFFRACTION	99.871
1.463-1.508	0.27	179	0.265	3597	X-RAY DIFFRACTION	99.5518
1.508-1.557	0.269	172	0.242	3457	X-RAY DIFFRACTION	98.8828
1.557-1.612	0.263	160	0.236	3344	X-RAY DIFFRACTION	98.8992
1.612-1.673	0.274	170	0.241	3230	X-RAY DIFFRACTION	98.7511
1.673-1.741	0.276	170	0.233	3093	X-RAY DIFFRACTION	98.6993
1.741-1.818	0.255	166	0.222	2960	X-RAY DIFFRACTION	98.8615
1.818-1.907	0.248	156	0.225	2743	X-RAY DIFFRACTION	96.0888
1.907-2.01	0.255	129	0.234	2562	X-RAY DIFFRACTION	93.4375
2.01-2.132	0.279	118	0.224	2496	X-RAY DIFFRACTION	96.4576
2.132-2.279	0.235	107	0.201	2155	X-RAY DIFFRACTION	88.9851
2.279-2.461	0.247	124	0.208	2175	X-RAY DIFFRACTION	96.475
2.461-2.696	0.251	89	0.208	2002	X-RAY DIFFRACTION	95.8295
2.696-3.013	0.218	90	0.21	1738	X-RAY DIFFRACTION	93.028
3.013-3.478	0.277	71	0.234	1347	X-RAY DIFFRACTION	80.3855
3.478-4.257	0.237	36		731	X-RAY DIFFRACTION	51.8243
4.257-6.008	0.346	31	0.273	530	X-RAY DIFFRACTION	49.7782
6.008-10	0.182	15		219	X-RAY DIFFRACTION	36.7347

Refinement TLS params.

Method: refined / Origin x: -20.4273 Å / Origin y: -12.5027 Å / Origin z: -13.3037 Å

	11	12	13	21	22	23	31	32	33
T	0.0405 Å²	-0.0259 Å²	-0.0058 Å²	-	0.0592 Å²	0.0192 Å²	-	-	0.0122 Å²
L	1.8822 °²	-0.3399 °²	-0.5049 °²	-	0.7538 °²	-0.0317 °²	-	-	0.1574 °²
S	0.045 Å °	0.0064 Å °	-0.0812 Å °	0.0662 Å °	-0.0587 Å °	0.0343 Å °	-0.0246 Å °	0.0071 Å °	0.0137 Å °

Refinement TLS group

Selection: ALL

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