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- PDB-8tww: Crystal structure of nitrile synthase AetD with substrate bound a... -

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Basic information

Entry
Database: PDB / ID: 8tww
TitleCrystal structure of nitrile synthase AetD with substrate bound and cofactor fully assembled
ComponentsAetD
KeywordsOXIDOREDUCTASE / nitrile synthase / non-heme iron enzyme / diiron enzyme
Function / homologyHaem oxygenase-like, multi-helical / metal ion binding / Chem-67I / : / AetD
Function and homology information
Biological speciesAetokthonos hydrillicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AetD
B: AetD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2859
Polymers61,2812
Non-polymers1,0037
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-56 kcal/mol
Surface area21600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.980, 88.131, 102.806
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid -2 through 124 or resid 126...
d_2ens_1(chain "B" and (resid -2 through 124 or resid 126...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERSERSERAA-2 - 12419 - 145
d_12ASPASPMSEMSEAA126 - 139147 - 160
d_13THRTHRPHEPHEAA141 - 147162 - 168
d_14ALAALAHISHISAA149 - 179170 - 200
d_15ASNASNALAALAAA185 - 238206 - 259
d_21SERSERSERSERBB-2 - 12419 - 145
d_22ASPASPMSEMSEBB108 - 139129 - 160
d_23THRTHRPHEPHEBB141 - 147162 - 168
d_24ALAALAALAALABB149 - 238170 - 259

NCS oper: (Code: givenMatrix: (-0.999949086615, -0.00477341593085, -0.00889036992855), (0.00985781204618, -0.273870873823, -0.961715949755), (0.00215585685457, -0.961754625137, 0.273903985567)Vector: ...NCS oper: (Code: given
Matrix: (-0.999949086615, -0.00477341593085, -0.00889036992855), (0.00985781204618, -0.273870873823, -0.961715949755), (0.00215585685457, -0.961754625137, 0.273903985567)
Vector: 0.168074226853, 39.5442523633, 30.0034420198)

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Components

#1: Protein AetD


Mass: 30640.727 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C11H10Br2N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.44 Å3/Da / Density % sol: 49.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 250 mM ammonium sulfate, 20% w/v PEG 3350

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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 23, 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→50 Å / Num. obs: 40402 / % possible obs: 98.7 % / Redundancy: 9 % / Biso Wilson estimate: 30.17 Å2 / CC1/2: 0.997 / Net I/σ(I): 13.19
Reflection shellResolution: 2→2.13 Å / Mean I/σ(I) obs: 4.2 / Num. unique obs: 6430 / CC1/2: 0.937

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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→46.98 Å / SU ML: 0.1852 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.5788
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2183 2021 5 %
Rwork0.1946 38377 -
obs0.1958 40398 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.92 Å2
Refinement stepCycle: LAST / Resolution: 2→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3958 0 39 263 4260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024105
X-RAY DIFFRACTIONf_angle_d0.60335552
X-RAY DIFFRACTIONf_chiral_restr0.0353603
X-RAY DIFFRACTIONf_plane_restr0.0032709
X-RAY DIFFRACTIONf_dihedral_angle_d10.9071523
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.070062546 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.26591400.23262647X-RAY DIFFRACTION97.86
2.05-2.110.24621430.2232739X-RAY DIFFRACTION100
2.11-2.170.23751440.20692722X-RAY DIFFRACTION100
2.17-2.240.23661450.20762746X-RAY DIFFRACTION99.93
2.24-2.320.23481450.20092747X-RAY DIFFRACTION99.86
2.32-2.420.231420.20052717X-RAY DIFFRACTION99.79
2.42-2.530.221460.20242752X-RAY DIFFRACTION98.74
2.53-2.660.24291420.20742745X-RAY DIFFRACTION99.72
2.66-2.830.24341470.21962760X-RAY DIFFRACTION99.79
2.83-3.040.22331450.21312777X-RAY DIFFRACTION100
3.04-3.350.23581460.19922777X-RAY DIFFRACTION99.9
3.35-3.830.20521320.18932456X-RAY DIFFRACTION87.49
3.83-4.830.16691440.15512831X-RAY DIFFRACTION99.93
4.83-46.980.22281600.19412961X-RAY DIFFRACTION99.65

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