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- PDB-8ayc: Scalindua brodae amxFabZ, I69G mutant -

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Basic information

Entry
Database: PDB / ID: 8ayc
TitleScalindua brodae amxFabZ, I69G mutant
ComponentsBeta-hydroxyacyl-(Acyl-carrier-protein) dehydratase
KeywordsLIPID BINDING PROTEIN / fatty acid biosynthesis
Function / homology
Function and homology information


3-hydroxyacyl-[acyl-carrier-protein] dehydratase / lyase activity
Similarity search - Function
Beta-hydroxydecanoyl thiol ester dehydrase, FabA/FabZ / FabA-like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
3-hydroxyacyl-[acyl-carrier-protein] dehydratase
Similarity search - Component
Biological speciesCandidatus Scalindua brodae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 Å
AuthorsDietl, A. / Barends, T.
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
DepositionSep 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Apr 26, 2023Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.3Feb 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


Theoretical massNumber of molelcules
Total (without water)15,4981
Polymers15,4981
Non-polymers00
Water97354
1
A: Beta-hydroxyacyl-(Acyl-carrier-protein) dehydratase
x 6


Theoretical massNumber of molelcules
Total (without water)92,9886
Polymers92,9886
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area13200 Å2
ΔGint-65 kcal/mol
Surface area30000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.598, 104.598, 79.797
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-251-

HOH

21A-253-

HOH

31A-254-

HOH

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Components

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


Mass: 15498.063 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Scalindua brodae amxFabZ I69G mutant / Source: (gene. exp.) Candidatus Scalindua brodae (bacteria) / Gene: SCABRO_02230 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B0EHL2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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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: 2.71 Å3/Da / Density % sol: 54.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.0 M Sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.746→39.39 Å / Num. obs: 15812 / % possible obs: 92.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 46.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Net I/σ(I): 19.1
Reflection shellResolution: 1.746→1.817 Å / Rmerge(I) obs: 0.876 / Num. unique obs: 793 / CC1/2: 0.423

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
STARANISOdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1U1Z

1u1z


Resolution: 1.75→39.39 Å / SU ML: 0.2071 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.7774
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2021 1582 10.01 %
Rwork0.1822 14230 -
obs0.1842 15812 92.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.89 Å2
Refinement stepCycle: LAST / Resolution: 1.75→39.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1017 0 0 54 1071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631042
X-RAY DIFFRACTIONf_angle_d0.8871408
X-RAY DIFFRACTIONf_chiral_restr0.0657168
X-RAY DIFFRACTIONf_plane_restr0.0052177
X-RAY DIFFRACTIONf_dihedral_angle_d19.7401384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80.3396510.3867460X-RAY DIFFRACTION33.25
1.8-1.870.34971340.31021200X-RAY DIFFRACTION86.74
1.87-1.940.29111480.23531337X-RAY DIFFRACTION95.99
1.94-2.030.23591530.18091384X-RAY DIFFRACTION100
2.03-2.140.20151550.16451389X-RAY DIFFRACTION99.87
2.14-2.270.20351570.17271406X-RAY DIFFRACTION100
2.27-2.450.20631550.16661400X-RAY DIFFRACTION100
2.45-2.690.22541540.18341393X-RAY DIFFRACTION99.94
2.69-3.080.22491570.19071408X-RAY DIFFRACTION100
3.08-3.880.19631580.17611417X-RAY DIFFRACTION99.81
3.88-39.390.18281600.18071436X-RAY DIFFRACTION97.67
Refinement TLS params.Method: refined / Origin x: -1.95733847078 Å / Origin y: 21.8162410012 Å / Origin z: 5.52083718642 Å
111213212223313233
T0.460099678931 Å2-3.29912100686E-5 Å20.0958527393898 Å2-0.410457700058 Å2-0.0564453903467 Å2--0.495262011912 Å2
L2.36923589875 °2-0.508970107383 °20.274292593245 °2-1.09408239759 °20.0128604130547 °2--1.16424306623 °2
S0.0848155744625 Å °-0.206857343973 Å °0.442080933686 Å °0.0365860417758 Å °0.160646342781 Å °-0.19550914368 Å °-0.177641309081 Å °0.0272800790941 Å °8.51558281609E-5 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 1 through 141)

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