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- PDB-8ayd: Anammox-specific FabZ from the annamox bacterium Kuenenia stuttga... -

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Basic information

Entry
Database: PDB / ID: 8ayd
TitleAnammox-specific FabZ from the annamox bacterium Kuenenia stuttgartiensis
Components3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
KeywordsBIOSYNTHETIC PROTEIN / lipid synthesis / ladderane / dehydratase
Function / homology
Function and homology information


(3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity / (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity / Lyases; Carbon-oxygen lyases; Hydro-lyases / (3R)-3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity
Similarity search - Function
Beta-hydroxydecanoyl thiol ester dehydrase, FabA/FabZ / FabA-like domain / HotDog domain superfamily
Similarity search - Domain/homology
3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
Similarity search - Component
Biological speciesCandidatus Kuenenia stuttgartiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDietl, A. / Barends, T.
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
AA: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
BA: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
CA: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ


Theoretical massNumber of molelcules
Total (without water)52,4203
Polymers52,4203
Non-polymers00
Water21612
1
AA: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
BA: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
CA: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ

AA: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
BA: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
CA: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ


  • defined by author&software
  • Evidence: gel filtration
  • 105 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)104,8406
Polymers104,8406
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area15520 Å2
ΔGint-81 kcal/mol
Surface area32610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.350, 75.350, 179.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4

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Components

#1: Protein 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ / Strongly similar to hydroxymyristoyl acyl carrier protein dehydratase


Mass: 17473.400 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Kuenenia stuttgartiensis (bacteria)
Gene: fabZ, fabZ_2, KsCSTR_20940, KSMBR1_3473, kuste3604 / Production host: Escherichia coli (E. coli)
References: UniProt: Q1Q2X5, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.3 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→47 Å / Num. obs: 13435 / % possible obs: 100 % / Redundancy: 12.5 % / Biso Wilson estimate: 75.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Net I/σ(I): 19
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.833 / Num. unique obs: 1223 / CC1/2: 0.844

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UIZ

1uiz


Resolution: 2.8→46.9 Å / SU ML: 0.4059 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.3014
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2843 690 5.14 %
Rwork0.2519 12742 -
obs0.2536 13432 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89.86 Å2
Refinement stepCycle: LAST / Resolution: 2.8→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3233 0 0 12 3245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00433290
X-RAY DIFFRACTIONf_angle_d0.97664448
X-RAY DIFFRACTIONf_chiral_restr0.0608542
X-RAY DIFFRACTIONf_plane_restr0.0061556
X-RAY DIFFRACTIONf_dihedral_angle_d9.0118428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.020.36861550.32982446X-RAY DIFFRACTION99.96
3.02-3.320.38151280.30582496X-RAY DIFFRACTION100
3.32-3.80.28571470.26812503X-RAY DIFFRACTION100
3.8-4.790.25761330.21812552X-RAY DIFFRACTION99.93
4.79-46.90.26141270.24432745X-RAY DIFFRACTION99.97
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)
14.6503782782-0.3786105468730.9961035598525.170154321120.7677572719893.26952019837-1.03602700302-0.3251545905720.614921159590.3580226452110.3798845818240.0172220304512-0.8820925978790.4156360511360.4893766667740.983815124677-0.0283808238998-0.2542875885920.5520170763880.008803670891110.440951211188.3604101655234.12694007816.54063187997
25.82827266518-0.983321130366-0.4776311953143.93345464537-0.1052375200253.07393180225-0.6114226485160.490467956477-0.443509568547-0.04088357805370.251323040913-0.0389610275540.2773544968470.3677848242840.343304661740.710321810632-0.07977350899280.2016165957360.682425410135-0.05829099558670.4749892839821.858819458411.7098305466-5.37375253405
32.549242440690.277283911862-0.4622191361482.70900622268-0.5932608965170.705909100398-0.567279673072-0.48772637425-1.498476756810.3134400898260.103515638931-0.2156901492710.5896020074360.5461277376420.07759863688741.128295465060.3107661540260.6138989094080.646822553050.1799927400061.2325464239514.4576444668-1.87230221676.83264071382
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'AA' and resid 1 through 146)AA1 - 146
2X-RAY DIFFRACTION2(chain 'BA' and resid 1 through 145)BA1 - 145
3X-RAY DIFFRACTION3(chain 'CA' and resid 10 through 154)CA10 - 154

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