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

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Basic information

Entry
Database: PDB / ID: 8twt
TitleCrystal structure of nitrile synthase AetD with substrate bound and cofactor partially assembled
ComponentsAetD
KeywordsOXIDOREDUCTASE / nitrile synthase / non-heme iron enzyme / diiron enzyme
Function / homologyHaem oxygenase-like, multi-helical / metal ion binding / Chem-67I / : / D-MALATE / SUCCINIC ACID / AetD
Function and homology information
Biological speciesAetokthonos hydrillicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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

Downloads & links

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Assembly

Deposited unit
A: AetD
B: AetD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,99511
Polymers60,6252
Non-polymers1,3709
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-23 kcal/mol
Surface area21350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.916, 86.089, 101.779
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 0 through 177 or resid 184...
d_2ens_1(chain "B" and (resid 0 through 191 or resid 193...

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_11METMETTHRTHRAA0 - 17721 - 198
d_12GLUGLUGLUGLUAA184 - 191205 - 212
d_13THRTHRALAALAAA193 - 203214 - 224
d_14GLUGLUHISHISAA205 - 228226 - 249
d_15SERSERALAALAAA230 - 238251 - 259
d_21METMETGLUGLUBB0 - 19121 - 212
d_22THRTHRALAALABB193 - 203214 - 224
d_23GLUGLUHISHISBB205 - 228226 - 249
d_24SERSERALAALABB230 - 238251 - 259

NCS oper: (Code: givenMatrix: (-0.999975411985, -0.00296266504397, 0.00635594530912), (0.00690991927522, -0.26181397087, 0.965093621196), (-0.00119517385566, 0.965113810529, 0.261828005161)Vector: 67. ...NCS oper: (Code: given
Matrix: (-0.999975411985, -0.00296266504397, 0.00635594530912), (0.00690991927522, -0.26181397087, 0.965093621196), (-0.00119517385566, 0.965113810529, 0.261828005161)
Vector: 67.0074148036, 9.61733171857, -7.35112906265)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein AetD


Mass: 30312.461 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

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Non-polymers , 6 types, 187 molecules

#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-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#4: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 100 mM MES monohydrate pH 6.0, 20% w/v 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 ...Details: 100 mM MES monohydrate pH 6.0, 20% w/v 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: SSRL / Beamline: BL9-2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2022
RadiationMonochromator: Double Crystal Si(111) and Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 25947 / % possible obs: 97.8 % / Redundancy: 12.2 % / Biso Wilson estimate: 30.6 Å2 / CC1/2: 0.998 / Net I/σ(I): 15.6
Reflection shellResolution: 2.3→2.44 Å / Mean I/σ(I) obs: 4 / Num. unique obs: 3958 / CC1/2: 0.927

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: SAD / Resolution: 2.3→39.64 Å / SU ML: 0.2096 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.2445
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2167 1296 5 %
Rwork0.1844 24638 -
obs0.186 25934 97.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.11 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3899 0 69 178 4146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00494074
X-RAY DIFFRACTIONf_angle_d0.79915504
X-RAY DIFFRACTIONf_chiral_restr0.043597
X-RAY DIFFRACTIONf_plane_restr0.0062705
X-RAY DIFFRACTIONf_dihedral_angle_d11.13821518
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.801541910505 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.390.25411310.21142491X-RAY DIFFRACTION91.2
2.39-2.50.24041440.21372732X-RAY DIFFRACTION98.97
2.5-2.630.2511420.20842738X-RAY DIFFRACTION98.83
2.63-2.790.2741410.22082672X-RAY DIFFRACTION96.9
2.79-3.010.23931450.21712755X-RAY DIFFRACTION99.18
3.01-3.310.24791460.21432759X-RAY DIFFRACTION98.84
3.31-3.790.23841450.17372755X-RAY DIFFRACTION98.47
3.79-4.770.14931470.14522804X-RAY DIFFRACTION98.7
4.77-39.640.19341550.16732932X-RAY DIFFRACTION99.07
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)
11.30784767714-0.236907481917-0.3475826590051.221172540880.3889360894472.73406738551-0.008470904612670.0578007248178-0.021853453367-0.0793804736474-0.01328357138550.08155388428890.120465419852-0.08269937761850.02500542072970.172899151048-0.0183550989784-0.006256824844540.1723226457090.02015886440310.19117570616119.428-0.49-16.362
21.18861030444-0.05265287894120.2604280594131.110247291780.3149026225041.33866840505-0.00960285677342-0.0625980685227-0.00352546318-0.04693700999590.0130961392753-0.1833452523290.1012247166110.204585197653-0.008846042131420.2249775405810.03439175159410.01092184100850.2634673264320.0103236647020.2576038909147.369-5.536-12.264
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 19:238 )A19 - 238
2X-RAY DIFFRACTION2( CHAIN B AND RESID 18:238 )B18 - 238

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