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- PDB-8ji6: Crystal structure of AetD in complex with L-tryptophan -

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Basic information

Entry
Database: PDB / ID: 8ji6
TitleCrystal structure of AetD in complex with L-tryptophan
ComponentsAetD
KeywordsMETAL BINDING PROTEIN / nitrile synthase / iron-dependent / L-tryptophan
Function / homologyHaem oxygenase-like, multi-helical / metal ion binding / : / NICKEL (II) ION / TRYPTOPHAN / AetD
Function and homology information
Biological speciesAetokthonos hydrillicola Thurmond2011 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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

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Assembly

Deposited unit
A: AetD
B: AetD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,23712
Polymers57,3012
Non-polymers93610
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-42 kcal/mol
Surface area20720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.289, 65.289, 116.145
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, 397 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-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2 / 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.: 387 / 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: 2.16 Å3/Da / Density % sol: 43.06 %
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: Apr 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 37037 / % possible obs: 96.1 % / Redundancy: 3.4 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.028 / Rpim(I) all: 0.016 / Rrim(I) all: 0.032 / Χ2: 0.707 / Net I/σ(I): 20.7 / Num. measured all: 127416
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.9-1.973.40.49937560.8270.9510.3030.5870.67797.4
1.97-2.053.30.31237240.9040.9750.1920.3680.72497
2.05-2.143.10.19936780.9530.9880.1250.2360.74496.1
2.14-2.253.30.14136880.9740.9930.0850.1660.79795.1
2.25-2.393.10.09535470.9840.9960.0580.1120.82293.3
2.39-2.583.30.05936640.9920.9980.0350.0690.77595.1
2.58-2.843.30.03836730.9950.9990.0230.0450.74795.4
2.84-3.253.60.02537620.9960.9990.0150.030.70397.5
3.25-4.093.90.0237960.9980.9990.0110.0230.70498.1
4.09-254.20.01637490.99810.0090.0190.48995.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→24.59 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.906 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22661 1724 4.8 %RANDOM
Rwork0.1741 ---
obs0.1767 33869 92.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.612 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2---0.29 Å20 Å2
3---0.58 Å2
Refinement stepCycle: 1 / Resolution: 1.9→24.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3878 0 45 387 4310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133998
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173710
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.645398
X-RAY DIFFRACTIONr_angle_other_deg1.3381.5788592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8255466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02522.447237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.22115728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2371528
X-RAY DIFFRACTIONr_chiral_restr0.0770.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024412
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02872
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_it1.9152.2711883
X-RAY DIFFRACTIONr_mcbond_other1.9152.2711882
X-RAY DIFFRACTIONr_mcangle_it2.9583.3942342
X-RAY DIFFRACTIONr_mcangle_other2.9583.3942343
X-RAY DIFFRACTIONr_scbond_it2.6952.6032115
X-RAY DIFFRACTIONr_scbond_other2.6952.6032115
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3883.7563056
X-RAY DIFFRACTIONr_long_range_B_refined6.02727.5484960
X-RAY DIFFRACTIONr_long_range_B_other5.91127.2274869
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.945 Å
RfactorNum. reflection% reflection
Rfree0.264 96 -
Rwork0.229 1979 -
obs--72.6 %

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