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- PDB-8ayb: anammox-specific FabZ from Scalindua brodae -

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Basic information

Entry
Database: PDB / ID: 8ayb
Titleanammox-specific FabZ from Scalindua brodae
ComponentsBeta-hydroxyacyl-(Acyl-carrier-protein) dehydratase
KeywordsBIOSYNTHETIC PROTEIN / ladderane / lipid biosynthesis / dehydratase
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDietl, A. / Barends, T.R.M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)724362-STePLADDEREuropean 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)15,5541
Polymers15,5541
Non-polymers00
Water1,06359
1
A: Beta-hydroxyacyl-(Acyl-carrier-protein) dehydratase
x 6


Theoretical massNumber of molelcules
Total (without water)93,3256
Polymers93,3256
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 area13170 Å2
ΔGint-76 kcal/mol
Surface area29150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.640, 104.640, 82.000
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-256-

HOH

21A-257-

HOH

31A-258-

HOH

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Components

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


Mass: 15554.169 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.: 59 / 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: 2.98 Å3/Da / Density % sol: 58.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 3.6 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: 1.033217 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033217 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 15501 / % possible obs: 96.1 % / Redundancy: 9.1 % / Biso Wilson estimate: 35.26 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Net I/σ(I): 19
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2237 / CC1/2: 0.847

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UIZ

1uiz


Resolution: 1.8→39.66 Å / SU ML: 0.1724 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.1664
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2035 776 5.01 %
Rwork0.1846 14725 -
obs0.1855 15501 96.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.49 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1021 0 0 59 1080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651040
X-RAY DIFFRACTIONf_angle_d0.86231405
X-RAY DIFFRACTIONf_chiral_restr0.0612169
X-RAY DIFFRACTIONf_plane_restr0.0047176
X-RAY DIFFRACTIONf_dihedral_angle_d18.559381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.910.24241120.23232125X-RAY DIFFRACTION84.73
1.91-2.060.27241240.19572346X-RAY DIFFRACTION92.41
2.06-2.270.22161320.18392518X-RAY DIFFRACTION99.33
2.27-2.60.23191340.18852539X-RAY DIFFRACTION100
2.6-3.270.21391350.20282561X-RAY DIFFRACTION100
3.27-39.660.18121390.17262636X-RAY DIFFRACTION99.89
Refinement TLS params.Method: refined / Origin x: -1.97843532239 Å / Origin y: 21.8411875824 Å / Origin z: 5.58195911304 Å
111213212223313233
T0.399550804767 Å20.0317172003692 Å20.16861175102 Å2-0.294398919073 Å2-0.0259926765813 Å2--0.409191063271 Å2
L2.15715380857 °2-0.374440777464 °20.154128155517 °2-0.740441205406 °2-0.0753082787114 °2--1.41005396975 °2
S0.113900532725 Å °-0.125719014766 Å °0.475417809691 Å °0.0398453008206 Å °0.23130591784 Å °-0.113724395038 Å °-0.248276639254 Å °-0.0563207882233 Å °0.0854996134574 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 1 through 141)

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