[English] 日本語
Yorodumi
- PDB-6riw: PfaC Keto synthase-Chain length factor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6riw
TitlePfaC Keto synthase-Chain length factor
ComponentsORF10
KeywordsPUFA synthase / PKS synthase / Ketosynthase / Chain Length Factor
Function / homology
Function and homology information


trans-2-decenoyl-[acyl-carrier protein] isomerase / trans-2-decenoyl-acyl-carrier-protein isomerase activity / (3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity / (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity / (3R)-3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
Beta-hydroxyacyl-(acyl-carrier-protein) dehydratase FabA / Beta-hydroxydecanoyl thiol ester dehydrase, FabA/FabZ / FabA-like domain / HotDog domain superfamily / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal ...Beta-hydroxyacyl-(acyl-carrier-protein) dehydratase FabA / Beta-hydroxydecanoyl thiol ester dehydrase, FabA/FabZ / FabA-like domain / HotDog domain superfamily / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like
Similarity search - Domain/homology
3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabA
Similarity search - Component
Biological speciesMoritella marina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSantin, O. / Moncalian, G.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPGC2018-093885-B-I00 Spain
CitationJournal: Biochemistry / Year: 2020
Title: Structure and Mechanism of the Ketosynthase-Chain Length Factor Didomain from a Prototypical Polyunsaturated Fatty Acid Synthase.
Authors: Santin, O. / Yuet, K. / Khosla, C. / Moncalian, G.
History
DepositionApr 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 2.0Feb 24, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Experimental preparation / Other / Refinement description / Structure summary
Category: atom_site / atom_sites ...atom_site / atom_sites / cell / citation / citation_author / database_2 / diffrn / diffrn_detector / diffrn_source / entity / exptl / exptl_crystal / exptl_crystal_grow / pdbx_audit_support / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct_conf / struct_conn / struct_keywords / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen / symmetry
Item: _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] ..._atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_c / _cell.volume / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.database_code / _database_2.database_id / _diffrn.ambient_temp / _diffrn_detector.pdbx_collection_date / _diffrn_detector.type / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type / _entity.pdbx_number_of_molecules / _exptl.crystals_number / _exptl_crystal.density_percent_sol / _exptl_crystal_grow.pH / _exptl_crystal_grow.pdbx_details / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly_prop.value / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_R_Free_selection_details / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _reflns.B_iso_Wilson_estimate / _reflns.number_obs / _reflns.pdbx_CC_half / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_netI_over_sigmaI / _reflns.pdbx_redundancy / _reflns.percent_possible_obs / _reflns_shell.Rmerge_I_obs / _reflns_shell.d_res_low / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _software.classification / _software.name / _software.version / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_keywords.pdbx_keywords / _struct_keywords.text / _symmetry.space_group_name_Hall
Revision 2.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ORF10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,3522
Polymers108,3281
Non-polymers241
Water9,224512
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-9 kcal/mol
Surface area29800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.240, 90.830, 132.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

-
Components

#1: Protein ORF10 /


Mass: 108327.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moritella marina (bacteria) / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Rosetta / References: UniProt: Q9RA19
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 512 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 20% 10,000 polyethylene glycol, 0.1 M HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.127 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.85→27.05 Å / Num. obs: 80533 / % possible obs: 99.3 % / Redundancy: 4.2 % / Biso Wilson estimate: 20.38 Å2 / CC1/2: 0.863 / Rmerge(I) obs: 0.069 / Net I/σ(I): 37.83
Reflection shellResolution: 1.85→1.916 Å / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 2.62 / Num. unique obs: 11547 / CC1/2: 0.559

-
Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MZ0

4mz0


Resolution: 1.85→74.9 Å / SU ML: 0.1654 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.9299
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1899 4016 4.99 %
Rwork0.1632 76514 -
obs0.1646 80530 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.29 Å2
Refinement stepCycle: LAST / Resolution: 1.85→74.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6933 0 1 512 7446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817058
X-RAY DIFFRACTIONf_angle_d0.8939574
X-RAY DIFFRACTIONf_chiral_restr0.05761093
X-RAY DIFFRACTIONf_plane_restr0.00541258
X-RAY DIFFRACTIONf_dihedral_angle_d11.5263964
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.24381270.21452620X-RAY DIFFRACTION99.42
1.87-1.890.27071270.21312633X-RAY DIFFRACTION99.53
1.89-1.920.23771400.19712590X-RAY DIFFRACTION98.81
1.92-1.940.23871440.18712518X-RAY DIFFRACTION96.66
1.94-1.970.22561460.18162568X-RAY DIFFRACTION98.05
1.97-20.20421560.18032610X-RAY DIFFRACTION99.46
2-2.030.23751200.17252622X-RAY DIFFRACTION99.49
2.03-2.060.24131210.1692658X-RAY DIFFRACTION99.71
2.06-2.090.20371430.16072574X-RAY DIFFRACTION99.16
2.09-2.130.18831210.15942633X-RAY DIFFRACTION99.35
2.13-2.170.18211060.16132672X-RAY DIFFRACTION99.64
2.17-2.210.19171290.15892610X-RAY DIFFRACTION99.56
2.21-2.260.19691160.15922655X-RAY DIFFRACTION99.5
2.26-2.30.21271450.16442627X-RAY DIFFRACTION99.28
2.3-2.360.18851280.16212587X-RAY DIFFRACTION97.52
2.36-2.420.18711470.16392578X-RAY DIFFRACTION98.84
2.42-2.480.19831450.1692636X-RAY DIFFRACTION99.32
2.48-2.560.19411450.16892626X-RAY DIFFRACTION99.35
2.56-2.640.19791490.17022622X-RAY DIFFRACTION99.57
2.64-2.730.23541210.16972673X-RAY DIFFRACTION99.61
2.73-2.840.19031430.16782644X-RAY DIFFRACTION99.68
2.84-2.970.20161610.17412639X-RAY DIFFRACTION99.75
2.97-3.130.2261430.16982623X-RAY DIFFRACTION98.36
3.13-3.320.19411620.16742626X-RAY DIFFRACTION99.86
3.32-3.580.17681540.16122678X-RAY DIFFRACTION99.65
3.58-3.940.16621400.14822702X-RAY DIFFRACTION99.75
3.94-4.510.12121340.13312698X-RAY DIFFRACTION99.33
4.51-5.680.15891450.15092735X-RAY DIFFRACTION99.38
5.68-74.90.19391580.16732857X-RAY DIFFRACTION99.7

+
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