PDB-6l9t: Crystal structure of the complex of bovine lactoperoxidase with O...

ID or keywords:

Entry

Database: PDB / ID: 6l9t

Title

Crystal structure of the complex of bovine lactoperoxidase with OSCN at 1.89 A resolution

Components

Lactoperoxidase

Keywords

OXIDOREDUCTASE /

lactoperoxidase

Function / homology

Function and homology information

Events associated with phagocytolytic activity of PMN cells / thiocyanate peroxidase activity /

lactoperoxidase activity /

peroxidase / hydrogen peroxide catabolic process /

peroxidase activity / antibacterial humoral response / response to oxidative stress / defense response to bacterium /

calcium ion binding ...
Similarity search - Function

Biological species

Bos taurus (cattle)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.89 Å

Authors

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

Citation

Journal: To Be Published
Title: Crystal structure of the complex of bovine lactoperoxidase with OSCN at 1.89 A resolution
Authors: Singh, P.K. / Kaur, P. / Sharma, S. / Singh, T.P.

History

Deposition	Nov 11, 2019	Deposition site: PDBJ / Processing site: PDBJ
Supersession	Sep 16, 2020	ID: 3OGW
Revision 1.0	Sep 16, 2020	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 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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PDBx/mmCIF format	6l9t.cif.gz	161.3 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l9/6l9t ftp://data.pdbj.org/pub/pdb/validation_reports/l9/6l9t	HTTPS FTP

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Related structure data

Related structure data	3ogw PDB Unreleased entryS S: Starting model for refinement
Similar structure data	7c75-d 6l32-d 6lrn-2 6l5g-d 5hpw-3 3gc1-d 6ky7-d 6lrn-1 2eha-1 7dn7-d 6kmk-d 4ljj-d 2e9e-2 3ogw-d 4msf-d 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	#17 - May 2001 Cyclooxygenase similarity (5) #190 - Oct 2015 Two-component Systems similarity (1)

Deposited unit

A: Lactoperoxidase

hetero molecules

72.8 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)	53.990, 79.930, 76.310
Angle α, β, γ (deg.)	90.000, 102.180, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 1 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 (cattle) / References: UniProt: P80025, peroxidase

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Sugars , 2 types, 4 molecules

#2: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide

/ Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}	LINUCS	PDB-CARE

#6: 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 /

N-Acetylglucosamine

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / 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 , 7 types, 594 molecules

#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical	ChemComp-IOD / IODIDE ION / Iodide Mass: 126.904 Da / Num. of mol.: 19 Source method: isolated from a genetically manipulated source Formula: I
#8: Chemical	ChemComp-SCN / THIOCYANATE ION / Thiocyanate Mass: 58.082 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CNS
#9: Chemical	ChemComp-OSM / 1-(OXIDOSULFANYL)METHANAMINE Mass: 79.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH₅NOS / Feature type: SUBJECT OF INVESTIGATION
#10: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 562 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.37 Å³/Da / Density % sol: 48.14 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: Ammonium Iodide, PEG3350, pH6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K PH range: 5-8

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
Detector	Type: MARRESEARCH / Detector: CCD / Date: May 13, 2010 / Details: mirror
Radiation	Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 1.89→74.59 Å / Num. obs: 50831 / % possible obs: 99.4 % / Redundancy: 8.2 % / R_sym value: 0.091 / Net I/σ(I): 10.8
Reflection shell	Resolution: 1.89→1.94 Å / Num. unique obs: 3581 / R_sym value: 0.341 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
DENZO		data reduction
SCALEPACK		data scaling
CNS		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3ogw

3ogw
PDB Unreleased entry

Resolution: 1.89→35.325 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.913 / WR_factor R_free: 0.278 / WR_factor R_work: 0.217 / SU B: 4.554 / SU ML: 0.135 / Average fsc free: 0.8773 / Average fsc work: 0.9028 / Cross valid method: FREE R-VALUE / ESU R: 0.181 / ESU R Free: 0.172
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2637	2579	5.077 %
R_work	0.2055	48223	-
all	0.208	-	-
obs	-	50802	99.945 %

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: 33.677 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.998 Å²	0 Å²	-0.406 Å²
2-	-	-2.166 Å²	-0 Å²
3-	-	-	3.055 Å²

Refinement step

Cycle: LAST / Resolution: 1.89→35.325 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4771	0	178	562	5511

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.013	5077
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	4583
X-RAY DIFFRACTION	r_angle_refined_deg	1.745	1.689	6888
X-RAY DIFFRACTION	r_angle_other_deg	1.295	1.606	10654
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.152	5	594
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.242	21.841	277
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.324	15	825
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.371	15	38
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	635
X-RAY DIFFRACTION	r_chiral_restr_other	0.238	0.2	1
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	5622
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	1103
X-RAY DIFFRACTION	r_nbd_refined	0.243	0.2	1265
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.209	0.2	4857
X-RAY DIFFRACTION	r_nbtor_refined	0.168	0.2	2358
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	2153
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.247	0.2	445
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.175	0.2	8
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.16	0.2	26
X-RAY DIFFRACTION	r_nbd_other	0.253	0.2	81
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.265	0.2	16
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.128	0.2	1
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.113	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	3.07	3.44	2392
X-RAY DIFFRACTION	r_mcbond_other	3.076	3.445	2381
X-RAY DIFFRACTION	r_mcangle_it	4.863	5.16	2973
X-RAY DIFFRACTION	r_mcangle_other	4.86	5.165	2973
X-RAY DIFFRACTION	r_scbond_it	2.755	3.745	2685
X-RAY DIFFRACTION	r_scbond_other	2.755	3.745	2686
X-RAY DIFFRACTION	r_scangle_it	4.307	5.553	3915
X-RAY DIFFRACTION	r_scangle_other	4.306	5.553	3916
X-RAY DIFFRACTION	r_lrange_it	10.588	63.973	25620
X-RAY DIFFRACTION	r_lrange_other	10.588	63.972	25621

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 (%)
1.89-1.939	0.32	183	0.258	3583	X-RAY DIFFRACTION	99.9735
1.939-1.992	0.326	177	0.248	3461	X-RAY DIFFRACTION	99.9451
1.992-2.05	0.27	182	0.237	3363	X-RAY DIFFRACTION	99.9718
2.05-2.113	0.288	206	0.241	3222	X-RAY DIFFRACTION	100
2.113-2.182	0.313	183	0.23	3160	X-RAY DIFFRACTION	99.9701
2.182-2.259	0.25	167	0.218	3064	X-RAY DIFFRACTION	100
2.259-2.344	0.288	144	0.215	2982	X-RAY DIFFRACTION	99.9041
2.344-2.439	0.256	148	0.215	2844	X-RAY DIFFRACTION	100
2.439-2.548	0.292	124	0.22	2762	X-RAY DIFFRACTION	99.9654
2.548-2.672	0.279	143	0.212	2596	X-RAY DIFFRACTION	100
2.672-2.816	0.316	132	0.216	2515	X-RAY DIFFRACTION	99.9622
2.816-2.987	0.294	120	0.212	2360	X-RAY DIFFRACTION	99.9597
2.987-3.193	0.27	128	0.197	2212	X-RAY DIFFRACTION	99.9573
3.193-3.448	0.225	105	0.195	2071	X-RAY DIFFRACTION	100
3.448-3.776	0.229	100	0.174	1894	X-RAY DIFFRACTION	99.9499
3.776-4.221	0.233	96	0.175	1743	X-RAY DIFFRACTION	100
4.221-4.871	0.214	82	0.168	1521	X-RAY DIFFRACTION	100
4.871-5.96	0.254	79	0.192	1287	X-RAY DIFFRACTION	99.9268
5.96-8.401	0.255	56	0.212	1007	X-RAY DIFFRACTION	100
8-10	0.272	24	0.205	576	X-RAY DIFFRACTION	97.7199

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