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- PDB-7qv0: Covalent complex between Scalindua brodae amxFabZ and amxACP -

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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 / HotDog domain superfamily / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 2.69 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

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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

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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

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