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- PDB-8twn: Crystal structure of nitrile synthase AetD with substrate bound -

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Basic information

Entry
Database: PDB / ID: 8twn
TitleCrystal structure of nitrile synthase AetD with substrate bound
ComponentsAetD
KeywordsOXIDOREDUCTASE / nitrile synthase / non-heme iron enzyme / diiron enzyme
Function / homologyHaem oxygenase-like, multi-helical / metal ion binding / Chem-67I / D-MALATE / AetD
Function and homology information
Biological speciesAetokthonos hydrillicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.08 Å
AuthorsYe, N. / Drennan, C.L.
Funding support United States, 4items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM126982 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30-GM124165 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30-GM133894 United States
CitationJournal: Nat.Chem. / Year: 2024
Title: A single diiron enzyme catalyses the oxidative rearrangement of tryptophan to indole nitrile.
Authors: Adak, S. / Ye, N. / Calderone, L.A. / Duan, M. / Lubeck, W. / Schafer, R.J.B. / Lukowski, A.L. / Houk, K.N. / Pandelia, M.E. / Drennan, C.L. / Moore, B.S.
History
DepositionAug 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 2, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AetD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1373
Polymers30,6411
Non-polymers4962
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.554, 101.554, 129.094
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

#1: Protein AetD


Mass: 30640.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aetokthonos hydrillicola (bacteria) / Gene: aetD / Production host: Escherichia coli (E. coli) / References: UniProt: A0A861B387
#2: Chemical ChemComp-67I / (2S)-2-azanyl-3-[5,7-bis(bromanyl)-1H-indol-3-yl]propanoic acid


Mass: 362.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10Br2N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.14 Å3/Da / Density % sol: 60.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES monohydrate pH 6.0, 20% PEG 4000, 110 mM malonic acid, 15 mM ammonium citrate tribasic, 7.2 mM succinic acid, 18 mM DL-malic acid, 24 mM sodium acetate trihydrate, 30 mM sodium ...Details: 100 mM MES monohydrate pH 6.0, 20% PEG 4000, 110 mM malonic acid, 15 mM ammonium citrate tribasic, 7.2 mM succinic acid, 18 mM DL-malic acid, 24 mM sodium acetate trihydrate, 30 mM sodium formate, 9.6 mM ammonium tartrate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 20, 2022
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 22444 / % possible obs: 92.4 % / Redundancy: 9.1 % / Biso Wilson estimate: 42.89 Å2 / CC1/2: 0.995 / Net I/σ(I): 9.6
Reflection shellResolution: 2.08→2.21 Å / Num. unique obs: 3470 / CC1/2: 0.844

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: SAD / Resolution: 2.08→47.25 Å / SU ML: 0.2551 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.045
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2132 1122 5 %
Rwork0.1826 21316 -
obs0.1842 22438 92.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.75 Å2
Refinement stepCycle: LAST / Resolution: 2.08→47.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1973 0 26 98 2097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00592056
X-RAY DIFFRACTIONf_angle_d0.88292781
X-RAY DIFFRACTIONf_chiral_restr0.0425300
X-RAY DIFFRACTIONf_plane_restr0.0057357
X-RAY DIFFRACTIONf_dihedral_angle_d11.4385769
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.180.28781300.25842481X-RAY DIFFRACTION88.78
2.18-2.290.26541420.22182685X-RAY DIFFRACTION95.51
2.29-2.430.271420.21462687X-RAY DIFFRACTION94.87
2.43-2.620.29261410.21132678X-RAY DIFFRACTION94.5
2.62-2.880.25771400.20812674X-RAY DIFFRACTION93.74
2.89-3.30.24421410.20832671X-RAY DIFFRACTION92.9
3.3-4.160.1721400.1512670X-RAY DIFFRACTION91.77
4.16-47.250.18141460.16452770X-RAY DIFFRACTION89.31

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