[English] 日本語
Yorodumi
- PDB-3vf1: Structure of a calcium-dependent 11R-lipoxygenase suggests a mech... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vf1
TitleStructure of a calcium-dependent 11R-lipoxygenase suggests a mechanism for Ca-regulation
Components11R-lipoxygenase
KeywordsOXIDOREDUCTASE / LOX / PLAT / beta sandwich / C2-like domain / non-heme iron / conformational change / dioxygenase
Function / homology
Function and homology information


oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / iron ion binding / cytoplasm
Similarity search - Function
Lipoxygenase, mammalian / Lipoxygenase-1; domain 5 / Lipoxygenase-1; Domain 5 / Nuclear Transport Factor 2; Chain: A, - #60 / PLAT/LH2 domain / Lipoxygenase, conserved site / Lipoxygenases iron-binding region signature 2. / Lipoxygenase-1 / Lipoxygenase / Lipoxygenase, C-terminal ...Lipoxygenase, mammalian / Lipoxygenase-1; domain 5 / Lipoxygenase-1; Domain 5 / Nuclear Transport Factor 2; Chain: A, - #60 / PLAT/LH2 domain / Lipoxygenase, conserved site / Lipoxygenases iron-binding region signature 2. / Lipoxygenase-1 / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase / Lipoxygenase iron-binding catalytic domain profile. / Lipoxygenase homology 2 (beta barrel) domain / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain / PLAT domain profile. / Nuclear Transport Factor 2; Chain: A, / Roll / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
sucrose / : / 11R-lipoxygenase
Similarity search - Component
Biological speciesGersemia fruticosa (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.473 Å
AuthorsEek, P. / Jarving, R. / Jarving, I. / Gilbert, N.C. / Newcomer, M.E. / Samel, N.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structure of a Calcium-dependent 11R-Lipoxygenase Suggests a Mechanism for Ca2+ Regulation.
Authors: Eek, P. / Jarving, R. / Jarving, I. / Gilbert, N.C. / Newcomer, M.E. / Samel, N.
History
DepositionJan 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Jul 25, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 11R-lipoxygenase
B: 11R-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,0806
Polymers158,2842
Non-polymers7964
Water8,683482
1
A: 11R-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5403
Polymers79,1421
Non-polymers3982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 11R-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5403
Polymers79,1421
Non-polymers3982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.800, 148.710, 117.330
Angle α, β, γ (deg.)90.000, 119.160, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-932-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 0 - 679 / Label seq-ID: 19 - 698

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1CHAIN A AND (RESSEQ 0:679 ) AND (NOT ELEMENT H)AA
2CHAIN B AND (RESSEQ 0:679 ) AND (NOT ELEMENT H)BB

NCS oper: (Code: given
Matrix: (-0.995463, -0.004949, -0.095022), (-0.002316, -0.99709, 0.076193), (-0.095123, 0.076067, 0.992555)
Vector: 8.85724, -50.879601, 2.5505)

-
Components

#1: Protein 11R-lipoxygenase


Mass: 79141.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gersemia fruticosa (invertebrata) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2N410
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 482 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THIS IS DUE TO CDNA VARIATIONS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 11-12% PEG 3350, 15% sucrose, 0.1M bis-Tris HCl, pH 7.2, vapor diffusion, hanging drop, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 31, 2010
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.473→36.482 Å / Num. all: 59434 / Num. obs: 59434 / % possible obs: 97.1 % / Redundancy: 3 % / Rsym value: 0.072 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.473-2.542.30.4741.5863138060.47484.6
2.54-2.612.50.4011.8988139800.40190.2
2.61-2.682.90.3781.91214442020.37898.1
2.68-2.763.20.3262.21301741180.32699.5
2.76-2.863.20.2492.91288140510.24999.6
2.86-2.963.20.1953.71231638780.19599.5
2.96-3.073.20.1654.41169436740.16599.4
3.07-3.193.20.1225.91153736430.12299.4
3.19-3.333.20.0977.51093034590.09799.1
3.33-3.53.20.08191043632910.08199.1
3.5-3.693.20.06111.9984131120.06199.1
3.69-3.913.20.05114.1956730040.05198.9
3.91-4.183.20.04415.9876327630.04498.7
4.18-4.513.20.04216.1820626010.04298.6
4.51-4.953.10.03916.6737223640.03998.1
4.95-5.533.10.04115.4658021410.04197.6
5.53-6.383.10.04316580018770.04398
6.38-7.823.10.03518.9496616010.03597.2
7.82-11.063.10.02622.4380312110.02696.9
11.06-36.48230.02424.419616580.02491.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
PHENIXdev_849refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
xia2data reduction
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.473→36.482 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.6 / σ(F): 0 / Phase error: 23.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2281 1912 3.33 %
Rwork0.2019 --
obs0.2027 57423 93.69 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.236 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso max: 155.01 Å2 / Biso mean: 46.8301 Å2 / Biso min: 20.19 Å2
Baniso -1Baniso -2Baniso -3
1--2.8114 Å20 Å2-9.7208 Å2
2---5.0843 Å2-0 Å2
3---7.8957 Å2
Refinement stepCycle: LAST / Resolution: 2.473→36.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10880 0 48 482 11410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511216
X-RAY DIFFRACTIONf_angle_d0.59815242
X-RAY DIFFRACTIONf_chiral_restr0.0361664
X-RAY DIFFRACTIONf_plane_restr0.0021946
X-RAY DIFFRACTIONf_dihedral_angle_d11.4624116
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A5440X-RAY DIFFRACTIONPOSITIONAL0.005
12B5440X-RAY DIFFRACTIONPOSITIONAL0.005
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.473-2.53470.33571080.31693080318873
2.5347-2.60320.28551150.29633400351581
2.6032-2.67980.29731350.27863801393690
2.6798-2.76630.29381360.27243952408895
2.7663-2.86510.261380.25084070420896
2.8651-2.97980.30881430.23574026416996
2.9798-3.11530.2541420.22814135427797
3.1153-3.27950.24411350.21764131426698
3.2795-3.48480.26371470.20524125427298
3.4848-3.75360.19661440.18194168431298
3.7536-4.13090.20861470.16644140428798
4.1309-4.72750.16991390.15294198433798
4.7275-5.9520.18211410.17044141428297
5.952-36.48560.20191420.18454144428696

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more