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- PDB-6lco: Crystal structure of bovine lactoperoxidase with substrates thioc... -

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Basic information

Entry
Database: PDB / ID: 6lco
TitleCrystal structure of bovine lactoperoxidase with substrates thiocynate and iodide bound at the distal heme side at 1.99 A resolution.
ComponentsLactoperoxidase
KeywordsOXIDOREDUCTASE / Peroxide family
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 ...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 / heme binding / extracellular space / cytoplasm
Similarity search - Function
Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / IODIDE ION / 1-(OXIDOSULFANYL)METHANAMINE / THIOCYANATE ION / Lactoperoxidase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.995 Å
AuthorsViswanathan, V. / Sirohi, H.V. / Kushwaha, G.S. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (India)PDF/2018/000008 India
CitationJournal: To Be Published
Title: Crystal structure of bovine lactoperoxidase with substrates thiocynate and iodide bound at the distal heme side at 1.99 A resolution.
Authors: Viswanathan, V. / Sirohi, H.V. / Kushwaha, G.S. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionNov 19, 2019Deposition site: PDBJ / Processing site: PDBJ
SupersessionDec 4, 2019ID: 4NT3
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_type / chem_comp ...atom_type / chem_comp / 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 / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lactoperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,25434
Polymers67,7731
Non-polymers4,48133
Water7,080393
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-31 kcal/mol
Surface area24650 Å2
Unit cell
Length a, b, c (Å)54.270, 80.441, 76.599
Angle α, β, γ (deg.)90.000, 103.200, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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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.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: 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.: 3 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 7 types, 422 molecules

#3: 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
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CNS / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-OSM / 1-(OXIDOSULFANYL)METHANAMINE


Mass: 79.122 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: CH5NOS / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Ammonium Iodide, PEG 3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.99→39.11 Å / Num. obs: 40498 / % possible obs: 92.62 % / Redundancy: 4.5 % / Rsym value: 0.054 / Net I/σ(I): 9.8
Reflection shellResolution: 1.99→2.05 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.9 / Num. unique obs: 3186 / Rsym value: 0.495

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NT3

4nt3
PDB Unreleased entry


Resolution: 1.995→39.105 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.227 / SU ML: 0.186 / Cross valid method: FREE R-VALUE / ESU R: 0.241 / ESU R Free: 0.203
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2611 2014 4.973 %
Rwork0.2069 --
all0.21 --
obs-40498 92.622 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.358 Å2
Baniso -1Baniso -2Baniso -3
1--0.039 Å2-0 Å21.197 Å2
2---1.413 Å20 Å2
3---0.803 Å2
Refinement stepCycle: LAST / Resolution: 1.995→39.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4770 0 167 393 5330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135081
X-RAY DIFFRACTIONr_bond_other_d0.0080.0174606
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.6846891
X-RAY DIFFRACTIONr_angle_other_deg1.471.60310704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8055600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90921.871278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.60615830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2491538
X-RAY DIFFRACTIONr_chiral_restr0.0720.2633
X-RAY DIFFRACTIONr_chiral_restr_other1.3650.23
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025640
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021104
X-RAY DIFFRACTIONr_nbd_refined0.2240.21202
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.24736
X-RAY DIFFRACTIONr_nbtor_refined0.1670.22380
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.22112
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2346
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0870.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1490.211
X-RAY DIFFRACTIONr_nbd_other0.1990.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1550.211
X-RAY DIFFRACTIONr_mcbond_it3.8665.3382398
X-RAY DIFFRACTIONr_mcbond_other3.8555.3372387
X-RAY DIFFRACTIONr_mcangle_it5.7258.0012984
X-RAY DIFFRACTIONr_mcangle_other5.7258.0032982
X-RAY DIFFRACTIONr_scbond_it4.0055.6662683
X-RAY DIFFRACTIONr_scbond_other4.0045.6672684
X-RAY DIFFRACTIONr_scangle_it6.0198.3883904
X-RAY DIFFRACTIONr_scangle_other6.0198.3883905
X-RAY DIFFRACTIONr_lrange_it9.47262.8075946
X-RAY DIFFRACTIONr_lrange_other9.462.5095853
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.995-2.0470.341460.31728900.31831860.6650.67195.29190.241
2.047-2.1030.3081580.27629770.27831370.8030.79599.93620.209
2.103-2.1630.321450.27528900.27730380.7280.74399.90130.22
2.163-2.230.353870.33216630.33329580.1920.23259.16160.262
2.23-2.3030.727920.70517020.70628890.3340.37462.09760.635
2.303-2.3830.3331300.25726250.26127690.8350.86199.49440.204
2.383-2.4730.3061290.21325460.21726970.8520.89999.18430.169
2.473-2.5730.2961250.20724350.21125740.8690.90899.45610.167
2.573-2.6870.2661200.20823310.21124680.9030.91299.31120.174
2.687-2.8180.2951150.222300.20523550.9070.92399.57540.173
2.818-2.9690.2371070.17921610.18222800.9220.93799.47370.162
2.969-3.1480.3171080.19720050.20321230.8830.91899.5290.188
3.148-3.3640.2481100.18719030.1920310.9030.93199.11370.187
3.364-3.6310.252800.18314960.18618710.9110.93684.2330.187
3.631-3.9750.206860.16814120.1717190.9370.95387.14370.172
3.975-4.4380.175790.13714620.13915740.9640.96697.90340.154
4.438-5.1140.177750.13612770.13813800.9640.97197.9710.159
5.114-6.2360.204620.15911100.16111860.930.95698.81960.189
6.236-8.7090.214440.1538820.1569280.9530.9699.78450.185
8.709-39.1050.153160.1594870.1595540.9670.97290.79420.192

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