PDB-8bpu: X-ray structure of the adduct formed upon reaction of Lysozyme wi...

ID or keywords:

Entry

Database: PDB / ID: 8bpu

Title

X-ray structure of the adduct formed upon reaction of Lysozyme with [Ru2Cl(D-p-FPhF)(O2CCH3)3] (Structure 2)

Components

Lysozyme

Keywords

HYDROLASE / 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 / 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: 1.81 Å

Authors

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

Funding support

1items

Citation

Journal: Inorg.Chem. / Year: 2023
Title: Effect of Equatorial Ligand Substitution on the Reactivity with Proteins of Paddlewheel Diruthenium Complexes: Structural Studies.
Authors: Teran, A. / Ferraro, G. / Sanchez-Pelaez, A.E. / Herrero, S. / Merlino, A.

History

Deposition	Nov 17, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 28, 2023	Provider: repository / Type: Initial release
Revision 1.1	Feb 7, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2	Feb 14, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8bpu.cif.gz	47.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8bpu.ent.gz		Display	PDB format
PDBx/mmJSON format	8bpu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8bpu_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	8bpu_full_validation.pdf.gz	1.4 MB	Display
Data in XML	8bpu_validation.xml.gz	8.5 KB	Display
Data in CIF	8bpu_validation.cif.gz	11.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bp/8bpu ftp://data.pdbj.org/pub/pdb/validation_reports/bp/8bpu	HTTPS FTP

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Related structure data

Related structure data	8bphC 8bpjC 8bqmC 198lS S: Starting model for refinement 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

AAA: Lysozyme

hetero molecules

15.7 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)	78.360, 78.360, 37.510
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-369- HOH
2	1	AAA-371- HOH
3	1	AAA-373- HOH

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Protein , 1 types, 1 molecules AAA

#1: Protein	Lysozyme Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme

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Non-polymers , 5 types, 78 molecules

#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#4: Chemical	ChemComp-R2I / 9,11-bis(4-fluorophenyl)-2,4,6,8-tetraoxa-9,11-diaza-1$l^{4},5$l^{4}-diruthenatricyclo[3.3.3.0^{1,5}]undecane Mass: 526.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₅H₁₄F₂N₂O₄Ru₂ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-R2U / Ru2-(OH)6 cluster Mass: 304.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H₆O₆Ru₂ / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.01 Å³/Da / Density % sol: 38.77 %
Crystal grow	Temperature: 293 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: 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: 1.81→55.41 Å / Num. obs: 11121 / % possible obs: 99.5 % / Redundancy: 20 % / CC_1/2: 0.993 / R_merge(I) obs: 0.191 / Net I/σ(I): 11.2
Reflection shell	Resolution: 1.81→1.84 Å / R_merge(I) obs: 1.328 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 524 / CC_1/2: 0.874

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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
Starting model: 198L

198l

Resolution: 1.81→55.409 Å / Cor.coef. F_o:F_c: 0.937 / Cor.coef. F_o:F_c free: 0.896 / WR_factor R_free: 0.318 / WR_factor R_work: 0.253 / SU B: 4.911 / SU ML: 0.148 / Average fsc free: 0.8574 / Average fsc work: 0.8859 / Cross valid method: FREE R-VALUE / ESU R: 0.185 / ESU R Free: 0.176
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2894	532	4.828 %
R_work	0.2291	10488	-
all	0.232	-	-
obs	-	11020	99.038 %

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: 32.33 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.481 Å²	0 Å²	0 Å²
2-	-	-0.481 Å²	0 Å²
3-	-	-	0.963 Å²

Refinement step

Cycle: LAST / Resolution: 1.81→55.409 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1001	0	55	73	1129

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	1083
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.014	956
X-RAY DIFFRACTION	r_ext_dist_refined_d	0.008	0.01	2
X-RAY DIFFRACTION	r_angle_refined_deg	1.557	1.697	1475
X-RAY DIFFRACTION	r_angle_other_deg	1.347	1.593	2182
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.524	5	128
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.072	20.656	61
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.403	15	167
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.048	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	131
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1236
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	280
X-RAY DIFFRACTION	r_nbd_refined	0.223	0.2	251
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.201	0.2	911
X-RAY DIFFRACTION	r_nbtor_refined	0.177	0.2	520
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	504
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.215	0.2	64
X-RAY DIFFRACTION	r_metal_ion_refined	0.173	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.275	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.195	0.2	30
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.289	0.2	16
X-RAY DIFFRACTION	r_mcbond_it	2.397	3.138	515
X-RAY DIFFRACTION	r_mcbond_other	2.396	3.134	514
X-RAY DIFFRACTION	r_mcangle_it	3.343	4.707	642
X-RAY DIFFRACTION	r_mcangle_other	3.341	4.711	643
X-RAY DIFFRACTION	r_scbond_it	3.004	3.653	568
X-RAY DIFFRACTION	r_scbond_other	2.984	3.585	525
X-RAY DIFFRACTION	r_scangle_it	4.474	5.35	833
X-RAY DIFFRACTION	r_scangle_other	4.564	5.263	771
X-RAY DIFFRACTION	r_lrange_it	6.487	38.297	1294
X-RAY DIFFRACTION	r_lrange_other	6.44	38.088	1254

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
1.81-1.857	0.365	36	0.29	749	0.293	804	0.789	0.82	97.6368	0.268
1.857-1.908	0.358	35	0.298	722	0.301	776	0.8	0.806	97.5516	0.273
1.908-1.963	0.417	36	0.279	720	0.286	762	0.756	0.838	99.2126	0.256
1.963-2.023	0.274	37	0.275	680	0.275	737	0.856	0.84	97.2863	0.254
2.023-2.09	0.295	36	0.271	697	0.272	734	0.844	0.868	99.8638	0.26
2.09-2.163	0.283	23	0.243	666	0.245	693	0.883	0.886	99.4228	0.237
2.163-2.244	0.286	34	0.246	627	0.248	668	0.88	0.891	98.9521	0.236
2.244-2.336	0.398	31	0.232	618	0.24	655	0.805	0.904	99.084	0.236
2.336-2.44	0.289	38	0.243	580	0.246	620	0.875	0.894	99.6774	0.246
2.44-2.558	0.261	26	0.245	563	0.246	597	0.893	0.895	98.66	0.252
2.558-2.696	0.319	31	0.23	545	0.235	582	0.874	0.914	98.9691	0.251
2.696-2.86	0.287	25	0.231	509	0.234	535	0.905	0.911	99.8131	0.248
2.86-3.056	0.299	22	0.234	488	0.236	513	0.901	0.907	99.4152	0.255
3.056-3.3	0.36	30	0.231	455	0.238	485	0.821	0.919	100	0.254
3.3-3.614	0.255	21	0.217	429	0.218	453	0.894	0.935	99.3378	0.248
3.614-4.039	0.266	18	0.179	390	0.182	409	0.934	0.953	99.7555	0.212
4.039-4.659	0.199	18	0.163	347	0.164	365	0.94	0.962	100	0.222
4.659-5.696	0.238	18	0.201	300	0.203	318	0.927	0.952	100	0.262
5.696-8.014	0.389	9	0.233	249	0.238	258	0.871	0.937	100	0.296
8.014-55.409	0.231	8	0.33	154	0.324	163	0.958	0.897	99.3865	0.476

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Protein , 1 types, 1 molecules AAA

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