PDB-29mr: X-ray structure of the adduct formed upon reaction of Lysozyme wi...

ID or keywords:

Entry

Database: PDB / ID: 29mr

Title

X-ray structure of the adduct formed upon reaction of Lysozyme with [Ru2(D-p-FPhF)(O2CCH3)2(O2CO)]

Components

Lysozyme C

Keywords

METAL BINDING PROTEIN / ruthenium / protein interaction / metallodrug / diruthenium

Function / homology

Function and homology information

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

Biological species

Gallus gallus (chicken)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.42 Å

Authors

Teran, A. / Ferraro, G. / Merlino, A.

Funding support

1items

Citation

Journal: Inorg.Chem. / Year: 2026
Title: Protein Recognition and Amyloid Remodeling Governed by Paddlewheel Diruthenium Coordination Chemistry.
Authors: La Manna, S. / Florio, D. / Ferraro, G. / Policino, M.R. / Altieri, F. / Teran, A. / Herrero, S. / Merlino, A. / Marasco, D.

History

Deposition	Mar 23, 2026	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 2, 2026	Provider: repository / Type: Initial release
Revision 1.1	Sep 16, 2026	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	29mr.cif.gz	50.5 KB	Display	PDBx/mmCIF format
PDB format	pdb29mr.ent.gz		Display	PDB format
PDBx/mmJSON format	29mr.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/9m/29mr ftp://data.pdbj.org/pub/pdb/validation_reports/9m/29mr	HTTPS FTP

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Related structure data

Related structure data	29ljC 29mnC 29myC 29nxC 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	#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

A: Lysozyme C

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	77.830, 77.830, 37.200
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	A-326- HOH
2	1	A-345- HOH
3	1	A-423- HOH
4	1	A-425- HOH

#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-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-NO3 / NITRATE ION Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO₃
#4: Chemical	ChemComp-A1IQW / [Ru2-N,N'-diphenylformamidinate(O2CCH3)2(O2CO)] complex / Diruthenium complex Mass: 611.458 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₈H₁₅F₂N₂O₇Ru₂ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 126 / 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: 1.97 Å³/Da / Density % sol: 37.42 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 20% ethylene glycol, 0.1 M sodium acetate at pH 4.0, and 0.6 M sodium nitrate

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Data collection

Diffraction	Mean temperature: 100 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: Jun 17, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.34→38.92 Å / Num. obs: 26206 / % possible obs: 99.9 % / Redundancy: 12.9 % / CC_1/2: 1 / Net I/σ(I): 27
Reflection shell	Resolution: 1.34→1.36 Å / Num. unique obs: 1288 / CC_1/2: 0.808

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0431	refinement
autoPROC		data reduction
autoPROC		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.42→38.945 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.952 / SU B: 1.455 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.08
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2255	1167	5.273 %	RANDOM
R_work	0.1927	20965	-	-
all	0.194	-	-	-
obs	-	22132	99.896 %	-

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: 22.678 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.057 Å²	-0 Å²	0 Å²
2-	-	-0.057 Å²	-0 Å²
3-	-	-	0.114 Å²

Refinement step

Cycle: LAST / Resolution: 1.42→38.945 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1001	0	50	126	1177

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	1166
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1026
X-RAY DIFFRACTION	r_angle_refined_deg	2.024	1.833	1597
X-RAY DIFFRACTION	r_angle_other_deg	1.51	1.814	2347
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.396	5	144
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.555	5	14
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.965	10	189
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.264	10	57
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	155
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	1532
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	315
X-RAY DIFFRACTION	r_nbd_refined	0.249	0.2	256
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.205	0.2	910
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	539
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.091	0.2	551
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.199	0.2	80
X-RAY DIFFRACTION	r_metal_ion_refined	0.085	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.25	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.163	0.2	75
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.267	0.2	30
X-RAY DIFFRACTION	r_mcbond_it	2.188	2.222	555
X-RAY DIFFRACTION	r_mcbond_other	2.185	2.221	555
X-RAY DIFFRACTION	r_mcangle_it	3.091	4.003	706
X-RAY DIFFRACTION	r_mcangle_other	3.092	4.007	707
X-RAY DIFFRACTION	r_scbond_it	3.167	2.633	611
X-RAY DIFFRACTION	r_scbond_other	3.12	2.589	562
X-RAY DIFFRACTION	r_scangle_it	4.784	4.702	891
X-RAY DIFFRACTION	r_scangle_other	4.771	4.594	817
X-RAY DIFFRACTION	r_lrange_it	6.611	25.638	1397
X-RAY DIFFRACTION	r_lrange_other	6.518	23.41	1329

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
1.42-1.457	0.337	100	0.291	1510	0.294	1610	0.929	0.947	100	0.25
1.457-1.497	0.349	83	0.272	1490	0.276	1573	0.925	0.956	100	0.226
1.497-1.54	0.296	72	0.252	1437	0.254	1509	0.948	0.96	100	0.211
1.54-1.587	0.265	80	0.243	1396	0.244	1476	0.957	0.962	100	0.201
1.587-1.639	0.246	76	0.223	1356	0.224	1433	0.964	0.969	99.9302	0.186
1.639-1.697	0.262	70	0.234	1327	0.235	1398	0.958	0.966	99.9285	0.196
1.697-1.761	0.324	65	0.223	1283	0.228	1349	0.932	0.967	99.9259	0.192
1.761-1.832	0.274	56	0.212	1234	0.215	1291	0.952	0.971	99.9225	0.187
1.832-1.914	0.236	63	0.22	1188	0.22	1251	0.968	0.97	100	0.203
1.914-2.007	0.247	64	0.184	1133	0.187	1198	0.965	0.978	99.9165	0.178
2.007-2.115	0.196	55	0.178	1075	0.179	1130	0.975	0.98	100	0.178
2.115-2.243	0.219	57	0.177	1029	0.179	1087	0.971	0.981	99.908	0.184
2.243-2.397	0.146	58	0.169	969	0.168	1028	0.983	0.983	99.9027	0.184
2.397-2.589	0.204	68	0.169	880	0.171	949	0.975	0.982	99.8946	0.185
2.589-2.834	0.21	40	0.171	856	0.172	896	0.97	0.982	100	0.197
2.834-3.167	0.257	53	0.168	750	0.174	805	0.962	0.98	99.7515	0.193
3.167-3.653	0.232	41	0.163	681	0.166	724	0.96	0.985	99.7238	0.199
3.653-4.464	0.177	35	0.152	588	0.154	625	0.98	0.985	99.68	0.198
4.464-6.272	0.202	18	0.224	476	0.223	501	0.974	0.974	98.6028	0.292
6.272-38.945	0.299	13	0.305	299	0.305	313	0.968	0.939	99.6805	0.399

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