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- PDB-8ji2: Crystal structure of AetD in complex with 5,7-dibromo-L-tryptophan -

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Basic information

Entry
Database: PDB / ID: 8ji2
TitleCrystal structure of AetD in complex with 5,7-dibromo-L-tryptophan
ComponentsAetD
KeywordsMETAL BINDING PROTEIN / nitrile synthase / iron-dependent / 5 / 7-dibromo-L-tryptophan
Function / homologyHaem oxygenase-like, multi-helical / metal ion binding / Chem-67I / : / NICKEL (II) ION / AetD
Function and homology information
Biological speciesAetokthonos hydrillicola Thurmond2011 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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: Nat Commun / Year: 2023
Title: The structural and functional investigation into an unusual nitrile synthase.
Authors: Li, H. / Huang, J.W. / Dai, L. / Zheng, H. / Dai, S. / Zhang, Q. / Yao, L. / Yang, Y. / Yang, Y. / Min, J. / Guo, R.T. / Chen, C.C.
History
DepositionMay 26, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)58,91413
Polymers57,3012
Non-polymers1,61311
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-62 kcal/mol
Surface area21230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.227, 65.227, 116.859
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein AetD


Mass: 28650.547 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

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Non-polymers , 5 types, 303 molecules

#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-67I / (2S)-2-azanyl-3-[5,7-bis(bromanyl)-1H-indol-3-yl]propanoic acid


Mass: 362.017 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H10Br2N2O2 / 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
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.17 Å3/Da / Density % sol: 43.3 %
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: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: May 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.75→25 Å / Num. obs: 48871 / % possible obs: 99.7 % / Redundancy: 4.3 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.024 / Rrim(I) all: 0.049 / Χ2: 0.891 / Net I/σ(I): 18.9 / Num. measured all: 209153
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.75-1.814.60.64849050.8080.9450.3330.730.501100
1.81-1.894.60.39948780.9080.9760.2060.450.529100
1.89-1.974.50.25148800.960.990.1310.2840.59100
1.97-2.074.30.15548660.9790.9950.0840.1770.734100
2.07-2.24.30.10248830.990.9980.0550.1170.981100
2.2-2.374.20.07148750.9940.9990.0390.0821.04699.9
2.37-2.614.40.05649090.9970.9990.030.0641.187100
2.61-2.994.40.04748910.9970.9990.0250.0531.1899.7
2.99-3.773.90.03748670.9980.9990.0210.0421.18899.4
3.77-253.70.0349170.9980.9990.0180.0351.11698.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→22.64 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.702 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21945 2435 5 %RANDOM
Rwork0.1714 ---
obs0.17372 46392 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.196 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å20 Å2
2---0.51 Å20 Å2
3---1.02 Å2
Refinement stepCycle: 1 / Resolution: 1.75→22.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3886 0 66 292 4244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134029
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173727
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.6575447
X-RAY DIFFRACTIONr_angle_other_deg1.4611.5898629
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9045469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40922.436234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30915725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5371528
X-RAY DIFFRACTIONr_chiral_restr0.0870.2519
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024441
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02875
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_it2.9153.6181895
X-RAY DIFFRACTIONr_mcbond_other2.9153.6181895
X-RAY DIFFRACTIONr_mcangle_it3.8145.4162357
X-RAY DIFFRACTIONr_mcangle_other3.8135.4162358
X-RAY DIFFRACTIONr_scbond_it4.7544.132134
X-RAY DIFFRACTIONr_scbond_other4.7534.1292135
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1455.9773091
X-RAY DIFFRACTIONr_long_range_B_refined8.88743.2044858
X-RAY DIFFRACTIONr_long_range_B_other8.88242.9814812
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.752→1.797 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 195 -
Rwork0.251 3390 -
obs--99.03 %

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