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- PDB-6l2j: Crystal structure of yak lactoperoxidase at 1.93 A resolution. -

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Basic information

Entry
Database: PDB / ID: 6l2j
TitleCrystal structure of yak lactoperoxidase at 1.93 A resolution.
ComponentsLactoperoxidase
KeywordsOXIDOREDUCTASE / Peroxide family
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 / lactoperoxidase activity / peroxidase / peroxidase activity / hydrogen peroxide catabolic process / antibacterial humoral response / basolateral plasma membrane / response to oxidative stress ...Events associated with phagocytolytic activity of PMN cells / thiocyanate peroxidase activity / detection of chemical stimulus involved in sensory perception of bitter taste / lactoperoxidase activity / peroxidase / peroxidase activity / hydrogen peroxide catabolic process / antibacterial humoral response / basolateral plasma membrane / response to oxidative stress / defense response to bacterium / calcium ion binding / heme binding / extracellular space / metal ion binding / 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 / HYDROGEN PEROXIDE / THIOCYANATE ION / Lactoperoxidase / Lactoperoxidase
Similarity search - Component
Biological speciesBos mutus (wild yak)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.933 Å
AuthorsViswanathan, V. / Sharma, P. / Rani, C. / 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 yak lactoperoxidase at 1.93 A resolution.
Authors: Viswanathan, V. / Sharma, P. / Rani, C. / Sharma, S. / Singh, T.P.
History
DepositionOct 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag

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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)75,20962
Polymers67,6531
Non-polymers7,55661
Water11,476637
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.850, 78.920, 67.750
Angle α, β, γ (deg.)90.000, 92.950, 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 /


Mass: 67653.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos mutus (wild yak)
References: UniProt: L8ICE9, UniProt: P80025*PLUS, peroxidase

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Sugars , 3 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: 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: isolated from a genetically manipulated source
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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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, 694 molecules

#4: 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
#6: Chemical...
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CNS / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-OSM / 1-(OXIDOSULFANYL)METHANAMINE


Mass: 79.122 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH5NOS / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-PEO / HYDROGEN PEROXIDE / Hydrogen peroxide


Mass: 34.015 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: H2O2 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 637 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Sequence detailsAuthor stated the observed sequence mutations from PHE to SER at residues 161 and 254 occurred in ...Author stated the observed sequence mutations from PHE to SER at residues 161 and 254 occurred in the substrate diffusion channel.

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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: 2.13 Å3/Da / Density % sol: 42.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.2M AMMONIUM IODIDE, 20% PEG 3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, 298K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.93→53.84 Å / Num. obs: 42433 / % possible obs: 100 % / Redundancy: 3.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.04 / Rrim(I) all: 0.078 / Net I/σ(I): 14.3
Reflection shellResolution: 1.93→1.98 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 5 / Num. unique obs: 3098 / CC1/2: 0.935 / Rpim(I) all: 0.136 / Rrim(I) all: 0.258 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A4Y

6a4y


Resolution: 1.933→53.837 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.443 / SU ML: 0.1 / Cross valid method: FREE R-VALUE / ESU R: 0.163 / ESU R Free: 0.146
RfactorNum. reflection% reflection
Rfree0.1979 1503 3.542 %
Rwork0.1453 --
all0.147 --
obs-42433 99.991 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.698 Å2
Baniso -1Baniso -2Baniso -3
1--0.029 Å2-0 Å2-0.865 Å2
2---0.207 Å20 Å2
3---0.323 Å2
Refinement stepCycle: LAST / Resolution: 1.933→53.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4760 0 280 637 5677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135278
X-RAY DIFFRACTIONr_bond_other_d0.0030.0174836
X-RAY DIFFRACTIONr_angle_refined_deg1.691.7017176
X-RAY DIFFRACTIONr_angle_other_deg1.3551.62211258
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1175634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.53621.625283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.14915872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9791541
X-RAY DIFFRACTIONr_chiral_restr0.0880.2675
X-RAY DIFFRACTIONr_chiral_restr_other0.2210.210
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025780
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021134
X-RAY DIFFRACTIONr_nbd_refined0.2410.21283
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.25006
X-RAY DIFFRACTIONr_nbtor_refined0.1680.22453
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.22177
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2518
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0090.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1970.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2160.250
X-RAY DIFFRACTIONr_nbd_other0.2440.2142
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1520.241
X-RAY DIFFRACTIONr_mcbond_it2.2651.9552441
X-RAY DIFFRACTIONr_mcbond_other2.2441.9542418
X-RAY DIFFRACTIONr_mcangle_it3.8712.9193042
X-RAY DIFFRACTIONr_mcangle_other3.8632.923033
X-RAY DIFFRACTIONr_scbond_it2.0322.1682837
X-RAY DIFFRACTIONr_scbond_other2.0312.1682838
X-RAY DIFFRACTIONr_scangle_it3.2843.1944114
X-RAY DIFFRACTIONr_scangle_other3.2843.1944115
X-RAY DIFFRACTIONr_lrange_it6.99224.4836390
X-RAY DIFFRACTIONr_lrange_other6.99124.4836391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.933-1.9830.278970.1783001X-RAY DIFFRACTION100
1.983-2.0370.2211080.1592938X-RAY DIFFRACTION100
2.037-2.0960.2381090.172837X-RAY DIFFRACTION100
2.096-2.1610.2521040.152804X-RAY DIFFRACTION100
2.161-2.2320.223900.1552679X-RAY DIFFRACTION99.9639
2.232-2.310.2321010.1712596X-RAY DIFFRACTION100
2.31-2.3970.1811000.1312493X-RAY DIFFRACTION100
2.397-2.4950.194870.1322429X-RAY DIFFRACTION100
2.495-2.6060.174840.1232335X-RAY DIFFRACTION100
2.606-2.7330.218690.1412242X-RAY DIFFRACTION100
2.733-2.880.18840.142104X-RAY DIFFRACTION100
2.88-3.0540.213640.1452010X-RAY DIFFRACTION100
3.054-3.2650.195670.1421891X-RAY DIFFRACTION100
3.265-3.5260.188570.141759X-RAY DIFFRACTION100
3.526-3.8610.207750.1371604X-RAY DIFFRACTION100
3.861-4.3150.132490.1181459X-RAY DIFFRACTION100
4.315-4.980.138460.1271317X-RAY DIFFRACTION100
4.98-6.090.193510.1531091X-RAY DIFFRACTION100
6.09-8.5780.204410.169851X-RAY DIFFRACTION100
8.578-53.830.177200.203490X-RAY DIFFRACTION99.4152

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