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- PDB-8zvh: Crystal structure of AetD in complex with L-phenylalanine -

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Basic information

Entry
Database: PDB / ID: 8zvh
TitleCrystal structure of AetD in complex with L-phenylalanine
ComponentsAetD
KeywordsMETAL BINDING PROTEIN / nitrile synthase / iron-dependent / L-phenylalanine
Function / homologyHaem oxygenase-like, multi-helical / metal ion binding / : / NICKEL (II) ION / PHENYLALANINE / AetD
Function and homology information
Biological speciesAetokthonos hydrillicola Thurmond2011 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsLi, H. / Dai, L. / Zheng, H.B. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Febs J. / Year: 2024
Title: Structural and molecular insights of two unique enzymes involved in the biosynthesis of a natural halogenated nitrile.
Authors: Chen, C.C. / Li, H. / Huang, J.W. / Guo, R.T.
History
DepositionJun 11, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _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
B: AetD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,15111
Polymers57,4152
Non-polymers7369
Water7,512417
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-48 kcal/mol
Surface area20730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.043, 65.043, 116.211
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein AetD


Mass: 28707.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aetokthonos hydrillicola Thurmond2011 (bacteria)
Gene: aetD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A861B387
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.14 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.01 M nickel chloride, 20% PEG 2000 MME, 0.1 M Tris, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Aug 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 1.87→32.54 Å / Num. obs: 39895 / % possible obs: 99.4 % / Redundancy: 6.3 % / CC1/2: 0.999 / Net I/σ(I): 17.8
Reflection shellResolution: 1.87→1.9 Å / Num. unique obs: 1866 / CC1/2: 0.831

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SAINTdata scaling
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→32.54 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.381 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25043 2002 5.1 %RANDOM
Rwork0.19165 ---
obs0.19476 37561 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.003 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å20 Å2
2---0.51 Å20 Å2
3---1.01 Å2
Refinement stepCycle: 1 / Resolution: 1.87→32.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3852 0 31 417 4300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133956
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173680
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.645338
X-RAY DIFFRACTIONr_angle_other_deg1.341.5778523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4525463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09422.426235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.0615724
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8321528
X-RAY DIFFRACTIONr_chiral_restr0.0780.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024375
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02865
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6483.2821870
X-RAY DIFFRACTIONr_mcbond_other2.6463.2821869
X-RAY DIFFRACTIONr_mcangle_it3.7434.9072327
X-RAY DIFFRACTIONr_mcangle_other3.7424.9072328
X-RAY DIFFRACTIONr_scbond_it3.2343.5952086
X-RAY DIFFRACTIONr_scbond_other3.2333.5952086
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9445.2413011
X-RAY DIFFRACTIONr_long_range_B_refined6.57839.0494874
X-RAY DIFFRACTIONr_long_range_B_other6.51438.7384795
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.87→1.919 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 126 -
Rwork0.296 2843 -
obs--99.66 %

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