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- PDB-8ayi: Scalindua brodae amxFabZ H48N mutant -

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Basic information

Entry
Database: PDB / ID: 8ayi
TitleScalindua brodae amxFabZ H48N 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 / lipid A biosynthetic process / lyase activity / membrane / cytoplasm
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: 2.2 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

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Assembly

Deposited unit
A: Beta-hydroxyacyl-(Acyl-carrier-protein) dehydratase


Theoretical massNumber of molelcules
Total (without water)17,3481
Polymers17,3481
Non-polymers00
Water1086
1
A: Beta-hydroxyacyl-(Acyl-carrier-protein) dehydratase
x 6


Theoretical massNumber of molelcules
Total (without water)104,0896
Polymers104,0896
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 area13420 Å2
ΔGint-68 kcal/mol
Surface area29620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.160, 105.160, 79.399
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

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Components

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


Mass: 17348.135 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.72 Å3/Da / Density % sol: 54.78 %
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: 1.000001 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: 1.000001 Å / Relative weight: 1
ReflectionResolution: 1.955→31.582 Å / Num. obs: 11349 / % possible obs: 93 % / Redundancy: 6.7 % / Biso Wilson estimate: 61.34 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.059 / Net I/σ(I): 13.7
Reflection shellResolution: 1.955→2.039 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.437 / Num. unique obs: 568 / CC1/2: 0.271 / % possible all: 43.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
STARANISOdata scaling
PHENIX1.18.2_3874phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1U1Z

1u1z


Resolution: 2.2→31.58 Å / SU ML: 0.2221 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.4907
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2612 866 10 %
Rwork0.248 7797 -
obs0.2494 8663 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.11 Å2
Refinement stepCycle: LAST / Resolution: 2.2→31.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1013 0 0 6 1019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00781031
X-RAY DIFFRACTIONf_angle_d1.38681393
X-RAY DIFFRACTIONf_chiral_restr0.0606168
X-RAY DIFFRACTIONf_plane_restr0.0076175
X-RAY DIFFRACTIONf_dihedral_angle_d18.7591379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.340.29651430.3061294X-RAY DIFFRACTION100
2.34-2.520.34331440.31411290X-RAY DIFFRACTION100
2.52-2.770.29521440.29591301X-RAY DIFFRACTION99.93
2.77-3.170.34251440.28811292X-RAY DIFFRACTION99.93
3.17-40.2851450.24941300X-RAY DIFFRACTION99.45
4-31.580.21451460.221320X-RAY DIFFRACTION97.02
Refinement TLS params.Method: refined / Origin x: -2.03804716567 Å / Origin y: 21.8901085069 Å / Origin z: 5.48572001349 Å
111213212223313233
T0.527808779749 Å20.0487564708854 Å20.0790851728653 Å2-0.64213673101 Å2-0.0651542774484 Å2--0.567538470873 Å2
L4.91643179529 °2-2.25850900357 °2-1.23673715725 °2-2.2917742411 °20.220390835367 °2--0.7785419211 °2
S-0.0501894935463 Å °-0.768380504191 Å °0.462246719499 Å °-0.150969603572 Å °0.46414859467 Å °-0.22596494151 Å °-0.23782219281 Å °0.0724277789604 Å °0.0943143408973 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 1 through 141)

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