PDB-8y9x: Crystal structure of the complex of lactoperoxidase with four ino...

ID or keywords:

Entry

Database: PDB / ID: 8y9x

Title

Crystal structure of the complex of lactoperoxidase with four inorganic substrates, SCN, I, Br and Cl

Components

Lactoperoxidase

Keywords

OXIDOREDUCTASE

Function / homology

Function and homology information

Events associated with phagocytolytic activity of PMN cells / thiocyanate peroxidase activity / detection of chemical stimulus involved in sensory perception of bitter taste / peroxidase / lactoperoxidase activity / hydrogen peroxide catabolic process / peroxidase activity / antibacterial humoral response / response to oxidative stress / basolateral plasma membrane ...
Similarity search - Function

Biological species

Bos taurus (domestic cattle)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Viswanathan, V. / Singh, A.K. / Pandey, N. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.

Funding support

India, 1items

Citation

Journal: To Be Published
Title: Structural evidence for the order of preference of inorganic substrates in mammalian heme peroxidases: crystal structure of the complex of lactoperoxidase with four inorganic substrates, SCN, I, Br and Cl
Authors: Viswanathan, V. / Singh, A.K. / Pandey, N. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.

History

Deposition	Feb 7, 2024	Deposition site: PDBJ / Processing site: PDBJ
Supersession	Mar 13, 2024	ID: 8K5M
Revision 1.0	Mar 13, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 30, 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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PDBx/mmCIF format	8y9x.cif.gz	156.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8y9x_validation.pdf.gz	9.7 MB	Display	wwPDB validaton report
Full document	8y9x_full_validation.pdf.gz	9.8 MB	Display
Data in XML	8y9x_validation.xml.gz	29.7 KB	Display
Data in CIF	8y9x_validation.cif.gz	43.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y9/8y9x ftp://data.pdbj.org/pub/pdb/validation_reports/y9/8y9x	HTTPS FTP

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Related structure data

Related structure data	8k5m PDB Unreleased entryS S: Starting model for refinement
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	#17 - May 2001 Cyclooxygenase similarity (5) #190 - Oct 2015 Two-component Systems similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

A: Lactoperoxidase

hetero molecules

72.3 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)	53.350, 80.332, 73.391
Angle α, β, γ (deg.)	90.000, 103.940, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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Protein / Sugars , 2 types, 7 molecules A

#1: Protein

Lactoperoxidase / LPO

Mass: 67773.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural)

Bos taurus (domestic cattle) / References: UniProt: P80025, peroxidase

#9: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₈H₁₅NO₆ / Feature type: SUBJECT OF INVESTIGATION

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Non-polymers , 8 types, 434 molecules

#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical	ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-BR / BROMIDE ION Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₄H₁₀O₃ / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical	ChemComp-SCN / THIOCYANATE ION Mass: 58.082 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CNS / Feature type: SUBJECT OF INVESTIGATION
#10: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.25 Å³/Da / Density % sol: 45.39 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 0.2 M Ammonium iodide, 20%(w/v) PEG 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298 K

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Data collection

Diffraction	Mean temperature: 298 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
Detector	Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 21, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 1.99→43.521 Å / Num. obs: 39294 / % possible obs: 96.7 % / Redundancy: 6.2 % / R_sym value: 0.082 / Net I/σ(I): 29.8
Reflection shell	Resolution: 1.99→2.05 Å / Mean I/σ(I) obs: 4.3 / Num. unique obs: 3044 / R_sym value: 0.31 / % possible all: 77

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 8K5M

8k5m
PDB Unreleased entry

Resolution: 2→43.521 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.934 / WR_factor R_free: 0.182 / WR_factor R_work: 0.143 / SU B: 3.736 / SU ML: 0.104 / Average fsc free: 0.9733 / Average fsc work: 0.9842 / Cross valid method: FREE R-VALUE / ESU R: 0.181 / ESU R Free: 0.152
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1951	1971	5.016 %
R_work	0.1506	37323	-
all	0.153	-	-
obs	-	39294	96.496 %

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: 29.645 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.035 Å²	-0 Å²	-0.01 Å²
2-	-	0.055 Å²	0 Å²
3-	-	-	-0.013 Å²

Refinement step

Cycle: LAST / Resolution: 2→43.521 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4742	0	205	407	5354

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	5095
X-RAY DIFFRACTION	r_bond_other_d	0.013	0.016	4761
X-RAY DIFFRACTION	r_angle_refined_deg	1.684	1.848	6897
X-RAY DIFFRACTION	r_angle_other_deg	0.783	1.77	10974
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.873	5	597
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.812	5	37
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.041	10	826
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.321	10	236
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	730
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	6002
X-RAY DIFFRACTION	r_gen_planes_other	0.011	0.02	1219
X-RAY DIFFRACTION	r_nbd_refined	0.227	0.2	1112
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.213	0.2	4688
X-RAY DIFFRACTION	r_nbtor_refined	0.183	0.2	2451
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.111	0.2	2610
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.181	0.2	332
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.047	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.347	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.313	0.2	93
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.207	0.2	17
X-RAY DIFFRACTION	r_mcbond_it	3.283	3.01	2384
X-RAY DIFFRACTION	r_mcbond_other	3.273	3.008	2379
X-RAY DIFFRACTION	r_mcangle_it	5.334	5.401	2971
X-RAY DIFFRACTION	r_mcangle_other	5.335	5.402	2972
X-RAY DIFFRACTION	r_scbond_it	3.463	3.347	2711
X-RAY DIFFRACTION	r_scbond_other	3.463	3.348	2711
X-RAY DIFFRACTION	r_scangle_it	5.743	6.002	3924
X-RAY DIFFRACTION	r_scangle_other	5.743	6.004	3924
X-RAY DIFFRACTION	r_lrange_it	9.892	31.535	5871
X-RAY DIFFRACTION	r_lrange_other	9.869	31.54	5869

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
2-2.052	0.237	106	0.201	2248	0.203	3044	0.964	0.969	77.3325	0.156
2.052-2.108	0.245	122	0.197	2357	0.199	2867	0.959	0.972	86.4667	0.149
2.108-2.169	0.223	124	0.175	2492	0.177	2816	0.96	0.979	92.8977	0.135
2.169-2.235	0.199	133	0.166	2582	0.168	2792	0.974	0.981	97.2421	0.127
2.235-2.308	0.194	133	0.147	2497	0.15	2655	0.977	0.986	99.0584	0.118
2.308-2.389	0.217	121	0.149	2443	0.153	2568	0.967	0.986	99.8442	0.122
2.389-2.479	0.173	138	0.132	2367	0.135	2507	0.983	0.989	99.9202	0.11
2.479-2.58	0.188	114	0.127	2287	0.13	2404	0.978	0.99	99.8752	0.108
2.58-2.694	0.192	118	0.137	2193	0.14	2317	0.975	0.988	99.741	0.118
2.694-2.825	0.211	120	0.146	2080	0.15	2211	0.971	0.987	99.5025	0.126
2.825-2.977	0.184	113	0.142	1988	0.145	2103	0.978	0.988	99.9049	0.129
2.977-3.157	0.179	98	0.148	1871	0.15	1973	0.979	0.987	99.7973	0.136
3.157-3.374	0.19	112	0.146	1750	0.148	1864	0.978	0.987	99.8927	0.14
3.374-3.642	0.2	97	0.152	1661	0.155	1760	0.973	0.986	99.8864	0.15
3.642-3.987	0.168	68	0.134	1544	0.135	1612	0.981	0.989	100	0.134
3.987-4.453	0.167	63	0.127	1402	0.129	1467	0.988	0.99	99.8637	0.133
4.453-5.133	0.198	73	0.149	1215	0.152	1290	0.979	0.988	99.845	0.162
5.133-6.265	0.216	48	0.177	1032	0.179	1081	0.971	0.983	99.9075	0.19
6.265-8.77	0.221	46	0.174	832	0.176	879	0.958	0.982	99.8862	0.195
8.77-43.521	0.169	24	0.177	482	0.177	507	0.984	0.982	99.8028	0.204

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