PDB-9ruv: X-ray structure of the adduct formed upon reaction of dirhodium-t...

ID or keywords:

Entry

Database: PDB / ID: 9ruv

Title

X-ray structure of the adduct formed upon reaction of dirhodium-tetraacetate with lysozyme at body temperature

Components

Lysozyme C

Keywords

HYDROLASE / dirhodium compound / protein metalation / body temperature crystalography

Function / homology

Function and homology information

Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...
Similarity search - Function

Biological species

Gallus gallus (chicken)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.12 Å

Authors

Tito, G. / Ferraro, G. / Merlino, A.

Funding support

Italy, 1items

Citation

Journal: Int J Mol Sci / Year: 2025
Title: Dirhodium Tetraacetate Binding to Lysozyme at Body Temperature.
Authors: Tito, G. / Ferraro, G. / Merlino, A.

History

Deposition	Jul 5, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 13, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9ruv.cif.gz	43.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9ruv.ent.gz		Display	PDB format
PDBx/mmJSON format	9ruv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9ruv_validation.pdf.gz	2.8 MB	Display	wwPDB validaton report
Full document	9ruv_full_validation.pdf.gz	2.8 MB	Display
Data in XML	9ruv_validation.xml.gz	8.4 KB	Display
Data in CIF	9ruv_validation.cif.gz	10.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ru/9ruv ftp://data.pdbj.org/pub/pdb/validation_reports/ru/9ruv	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	#21 - Sep 2001 Antibodies similarity (3) #136 - Apr 2011 Nanobodies similarity (3) #222 - Jun 2018 Proteins and Nanoparticles similarity (3) #9 - Sep 2000 Lysozyme similarity (3) #142 - Oct 2011 PDB Pioneers similarity (3)

Deposited unit

AAA: Lysozyme C

hetero molecules

15.1 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)	80.430, 80.430, 36.140
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	AAA-201- RH

#1: Protein	Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical	ChemComp-RH / Rhodium Mass: 102.906 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Rh / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 2.04 Å³/Da / Density % sol: 39.68 %
Crystal grow	Temperature: 310 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.0 M sodium formate, 0.1 M hepes buffer pH 7.5

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Data collection

Diffraction	Mean temperature: 310 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.12→56.873 Å / Num. obs: 6617 / % possible obs: 94 % / Redundancy: 11.4 % / CC_1/2: 0.998 / R_merge(I) obs: 0.092 / Net I/σ(I): 13.2
Reflection shell	Resolution: 2.12→2.15 Å / Redundancy: 11.8 % / R_merge(I) obs: 2.788 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 342 / CC_1/2: 0.405 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
autoPROC		data reduction
autoPROC		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.12→56.873 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.936 / SU B: 6.973 / SU ML: 0.176 / Cross valid method: FREE R-VALUE / ESU R: 0.316 / ESU R Free: 0.238
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2612	332	5.096 %
R_work	0.1977	6183	-
all	0.201	-	-
obs	-	6515	91.4 %

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: 61.2 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.172 Å²	0 Å²	0 Å²
2-	-	-0.172 Å²	0 Å²
3-	-	-	0.344 Å²

Refinement step

Cycle: LAST / Resolution: 2.12→56.873 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1001	0	8	24	1033

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	1036
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.014	946
X-RAY DIFFRACTION	r_ext_dist_refined_d	0.133	0.01	16
X-RAY DIFFRACTION	r_angle_refined_deg	1.571	1.613	1424
X-RAY DIFFRACTION	r_angle_other_deg	1.355	1.595	2156
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.25	5	130
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.665	20.806	62
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.175	15	168
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.493	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	132
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1240
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	284
X-RAY DIFFRACTION	r_nbd_refined	0.23	0.2	231
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.202	0.2	910
X-RAY DIFFRACTION	r_nbtor_refined	0.166	0.2	497
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	509
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.184	0.2	36
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.007	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.191	0.2	6
X-RAY DIFFRACTION	r_nbd_other	0.188	0.2	26
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.102	0.2	7
X-RAY DIFFRACTION	r_mcbond_it	4.561	6.044	520
X-RAY DIFFRACTION	r_mcbond_other	4.554	6.036	519
X-RAY DIFFRACTION	r_mcangle_it	6.348	9.105	657
X-RAY DIFFRACTION	r_mcangle_other	6.084	9.068	651
X-RAY DIFFRACTION	r_scbond_it	5.656	6.723	516
X-RAY DIFFRACTION	r_scbond_other	5.645	6.724	516
X-RAY DIFFRACTION	r_scangle_it	9.512	10.026	780
X-RAY DIFFRACTION	r_scangle_other	8.783	9.952	772
X-RAY DIFFRACTION	r_lrange_it	10.548	70.668	1207
X-RAY DIFFRACTION	r_lrange_other	10.444	70.531	1205

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
2.12-2.175	0.316	21	0.253	382	0.256	506	0.835	0.878	79.6443	0.248
2.175-2.234	0.311	25	0.278	414	0.28	499	0.814	0.841	87.976	0.267
2.234-2.299	0.316	10	0.309	306	0.309	489	0.802	0.798	64.6217	0.285
2.299-2.37	0.246	17	0.324	433	0.321	466	0.836	0.79	96.5665	0.301
2.37-2.447	0.273	20	0.27	440	0.271	466	0.871	0.848	98.7124	0.243
2.447-2.533	0.367	23	0.262	414	0.268	437	0.827	0.877	100	0.227
2.533-2.629	0.253	24	0.24	407	0.241	433	0.933	0.911	99.5381	0.212
2.629-2.736	0.305	23	0.21	289	0.216	415	0.899	0.936	75.1807	0.175
2.736-2.857	0.196	14	0.193	392	0.193	406	0.934	0.942	100	0.171
2.857-2.996	0.288	24	0.184	364	0.189	388	0.888	0.947	100	0.161
2.996-3.158	0.219	14	0.192	346	0.193	360	0.938	0.945	100	0.176
3.158-3.349	0.274	22	0.195	333	0.2	355	0.914	0.944	100	0.191
3.349-3.579	0.355	7	0.184	257	0.188	319	0.857	0.95	82.7586	0.184
3.579-3.864	0.242	10	0.165	248	0.169	316	0.942	0.958	81.6456	0.178
3.864-4.231	0.203	21	0.157	234	0.16	288	0.957	0.964	88.5417	0.171
4.231-4.727	0.236	22	0.166	243	0.172	266	0.948	0.964	99.6241	0.198
4.727-5.452	0.313	14	0.197	220	0.203	234	0.911	0.957	100	0.234
5.452-6.662	0.21	11	0.171	193	0.173	204	0.956	0.956	100	0.205
6.662-9.358	0.365	8	0.184	161	0.19	169	0.908	0.967	100	0.237
9.358-56.873	0.247	2	0.24	107	0.24	110	1	0.957	99.0909	0.286

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