[English] 日本語
Yorodumi
- PDB-7qv0: Covalent complex between Scalindua brodae amxFabZ and amxACP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qv0
TitleCovalent complex between Scalindua brodae amxFabZ and amxACP
Components
  • Acyl carrier protein
  • Beta-hydroxyacyl-(Acyl-carrier-protein) dehydratase
KeywordsBIOSYNTHETIC PROTEIN / lipid biosynthesis / ladderane / acyl carrier protein / dehydratase / FabZ / ACP
Function / homology
Function and homology information


Beta-hydroxydecanoyl thiol ester dehydrase, FabA/FabZ / FabA-like domain / ACP-like / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. ...Beta-hydroxydecanoyl thiol ester dehydrase, FabA/FabZ / FabA-like domain / ACP-like / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-GC5 / Beta-hydroxyacyl-(Acyl-carrier-protein) dehydratase / Acyl carrier protein
Similarity search - Component
Biological speciesCandidatus Scalindua brodae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsBarends, T. / Dietl, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)724362European Union
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structures of an unusual 3-hydroxyacyl dehydratase (FabZ) from a ladderane-producing organism with an unexpected substrate preference.
Authors: Dietl, A. / Wellach, K. / Mahadevan, P. / Mertes, N. / Winter, S.L. / Kutsch, T. / Walz, C. / Schlichting, I. / Fabritz, S. / Barends, T.R.M.
History
DepositionJan 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 2.0Apr 26, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / citation_author / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn
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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _citation.journal_volume / _citation_author.name / _pdbx_struct_assembly_gen.asym_id_list
Revision 2.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-hydroxyacyl-(Acyl-carrier-protein) dehydratase
B: Beta-hydroxyacyl-(Acyl-carrier-protein) dehydratase
C: Beta-hydroxyacyl-(Acyl-carrier-protein) dehydratase
D: Acyl carrier protein
E: Acyl carrier protein
F: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7729
Polymers76,4086
Non-polymers1,3633
Water543
1
A: Beta-hydroxyacyl-(Acyl-carrier-protein) dehydratase
B: Beta-hydroxyacyl-(Acyl-carrier-protein) dehydratase
C: Beta-hydroxyacyl-(Acyl-carrier-protein) dehydratase
D: Acyl carrier protein
E: Acyl carrier protein
F: Acyl carrier protein
hetero molecules

A: Beta-hydroxyacyl-(Acyl-carrier-protein) dehydratase
B: Beta-hydroxyacyl-(Acyl-carrier-protein) dehydratase
C: Beta-hydroxyacyl-(Acyl-carrier-protein) dehydratase
D: Acyl carrier protein
E: Acyl carrier protein
F: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,54418
Polymers152,81712
Non-polymers2,7276
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Unit cell
Length a, b, c (Å)94.789, 94.789, 158.218
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 4 through 76 or resid 84 through 141 or resid 202 through 301))A4 - 76
121(chain 'A' and (resid 4 through 76 or resid 84 through 141 or resid 202 through 301))A84 - 141
131(chain 'A' and (resid 4 through 76 or resid 84 through 141 or resid 202 through 301))A202
141(chain 'A' and (resid 4 through 76 or resid 84 through 141 or resid 202 through 301))A301
251(chain 'B' and (resid 4 through 76 or resid 84 through 141 or resid 202 through 301))B4 - 76
261(chain 'B' and (resid 4 through 76 or resid 84 through 141 or resid 202 through 301))B84 - 141
271(chain 'B' and (resid 4 through 76 or resid 84 through 141 or resid 202 through 301))B202
281(chain 'B' and (resid 4 through 76 or resid 84 through 141 or resid 202 through 301))B301
391(chain 'C' and (resid 4 through 76 or resid 84 through 141 or resid 202 through 301))C4 - 76
3101(chain 'C' and (resid 4 through 76 or resid 84 through 141 or resid 202 through 301))C84 - 141
3111(chain 'C' and (resid 4 through 76 or resid 84 through 141 or resid 202 through 301))C202
3121(chain 'C' and (resid 4 through 76 or resid 84 through 141 or resid 202 through 301))C301
1132chain 'E'E2 - 84
2142chain 'D'D2 - 84
3152chain 'F'F2 - 84

NCS ensembles :
ID
1
2

-
Components

#1: Protein Beta-hydroxyacyl-(Acyl-carrier-protein) dehydratase


Mass: 15942.633 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Scalindua brodae (bacteria) / Gene: SCABRO_02230 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B0EHL2
#2: Protein Acyl carrier protein


Mass: 9526.851 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Scalindua brodae (bacteria) / Gene: SCABRO_02231 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B0EN18
#3: Chemical ChemComp-GC5 / S-[2-[3-[[(2R)-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (Z)-hex-2-enethioate


Mass: 454.475 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H31N2O8PS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.2 % / Description: needle-like
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 10% (w/v) PEG 3350, 0.2 M ammonium acetate, 0.1 M sodium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99988 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 2.49→45.4 Å / Num. obs: 17797 / % possible obs: 92.1 % / Redundancy: 7 % / Biso Wilson estimate: 76.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.9
Reflection shellResolution: 2.49→2.8 Å / Rmerge(I) obs: 0.942 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 927 / CC1/2: 0.683

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y52

6y52
PDB Unreleased entry


Resolution: 2.49→45.4 Å / SU ML: 0.1868 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 39.0634
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2718 904 5.08 %
Rwork0.2407 16893 -
obs0.2424 17797 60.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 134.77 Å2
Refinement stepCycle: LAST / Resolution: 2.49→45.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5179 0 84 3 5266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00545335
X-RAY DIFFRACTIONf_angle_d0.88097183
X-RAY DIFFRACTIONf_chiral_restr0.0533864
X-RAY DIFFRACTIONf_plane_restr0.0046903
X-RAY DIFFRACTIONf_dihedral_angle_d26.39052009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.650.5683180.5079294X-RAY DIFFRACTION6.49
2.65-2.850.3764470.3597795X-RAY DIFFRACTION17.49
2.85-3.140.36121030.31581895X-RAY DIFFRACTION41.32
3.14-3.590.29372310.27534381X-RAY DIFFRACTION94.43
3.59-4.520.25582240.21654702X-RAY DIFFRACTION99.84
4.52-45.40.26282810.23434826X-RAY DIFFRACTION99.61
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.29617704913-1.34508436774-1.516291906953.05702832317-1.638157221316.61227561950.0137409131435-0.3516767274580.1342316719570.0121674716104-0.157349256614-0.175373793571-0.5578760973040.170038504571-0.00403381779634-0.0276398770420.0346967818847-0.06660708839480.390622525328-0.0232211961090.1590405686641.413266589758.6832685035420.3658134123
25.32363330466-0.03782544907751.876103473852.6023495703-1.829488669455.74241506799-0.127255554207-0.3923570366110.2819887852470.283258337480.0382913931821-0.445931714041-0.6414576419450.866222536567-0.01029743448980.0523997971154-0.1773656773220.05469420741651.279572881140.2120389455150.5739669746739.36668250959.5289404451515.8482949783
35.844820403420.0948339150485-0.02888349777813.933429403891.116763237525.754592288620.0302942885813-0.13069630577-0.0315303537075-0.0324683756905-0.33508106914-0.31670619350.1161429514180.510545407373-0.02763417557810.006315377332370.1316176532970.1234612985110.6423830764890.2326858405920.30675927902723.97572920881.687874639883.73492493966
40.524066015638-0.574336532404-0.08028920519530.6274094244020.0403702392690.670861449975-0.8245085739420.8409097660860.51124343711-1.253457924050.691353681586-0.1550851709040.3922385776670.9980479567920.0001454450788592.09397090412-0.3160148957770.1710361442141.628112303640.478488680321.457154965637.462508140525.8032395628-11.9394662802
50.1776685865560.218839385938-0.1234461547570.266543320765-0.1487335153090.09676550567980.4214583974161.768768402750.104201377822-0.7502535326590.870248396004-1.12815661533-1.222023553830.121620934772-2.522609269E-81.847239006490.1968827470450.7105665550472.78384477831-0.3775791847932.259891235849.53629637841.17264136187-14.0518046972
60.461338326215-0.2487167721390.4319936846880.325135998134-0.1149432391570.4592697357880.142309150024-0.04776622161460.360086094639-0.6072704153090.7156753837082.087821377180.396362550904-0.8679227381091.24997858605E-81.04944525994-0.34159846395-0.2529668451551.99860261237-0.01865084297872.25070904527-25.2754361808-8.9383345843214.9832861151
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F

+
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