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- PDB-8jz6: Crystal structure of AetF in complex with FAD and NADP+ at 2.66 a... -

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Basic information

Entry
Database: PDB / ID: 8jz6
TitleCrystal structure of AetF in complex with FAD and NADP+ at 2.66 angstrom
ComponentsAetF
KeywordsFLAVOPROTEIN / halogenase / flavin-dependent / single-component / NADP+
Function / homologyFAD/NAD(P)-binding domain superfamily / nucleotide binding / metal ion binding / FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / AetF
Function and homology information
Biological speciesAetokthonos hydrillicola Thurmond2011 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsLi, H. / Dai, L. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of AetF in complex with FAD and NADP+ at 2.66 angstrom
Authors: Li, H. / Dai, L. / Chen, C.-C. / Guo, R.-T.
History
DepositionJul 4, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AetF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0853
Polymers78,5561
Non-polymers1,5292
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-9 kcal/mol
Surface area25070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.079, 75.469, 143.904
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AetF


Mass: 78556.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aetokthonos hydrillicola Thurmond2011 (bacteria)
Gene: aetF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A861B9Z9
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.08 Å3/Da / Density % sol: 40.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% PEG 6000, 0.1 M Tris pH 8.0, 8 mg/mL AetF (5 mM DTT)

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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: 2.66→25 Å / Num. obs: 19443 / % possible obs: 97 % / Redundancy: 4.4 % / CC1/2: 0.978 / CC star: 0.994 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.06 / Rrim(I) all: 0.129 / Χ2: 1.024 / Net I/σ(I): 7.2 / Num. measured all: 85248
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.66-2.754.30.51119670.8980.9730.2690.5810.65499.7
2.75-2.874.50.46719800.920.9790.2380.5270.70699.8
2.87-34.30.37519340.9450.9860.1980.4270.75299.7
3-3.154.60.31519640.9620.990.1570.3540.94499.6
3.15-3.354.40.21419780.9770.9940.110.2421.07699
3.35-3.614.60.14719370.9880.9970.0750.1661.15999
3.61-3.974.70.11119730.9910.9980.0570.1251.24998.7
3.97-4.544.50.08119110.9920.9980.0430.0931.29294.6
4.54-5.7140.06518830.9940.9980.0370.0761.25492.4
5.71-2540.05219160.9940.9990.030.061.18288.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→24.56 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.901 / SU B: 14.724 / SU ML: 0.303 / Cross valid method: THROUGHOUT / ESU R Free: 0.399 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27251 970 5 %RANDOM
Rwork0.19133 ---
obs0.1953 18420 95.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.177 Å2
Baniso -1Baniso -2Baniso -3
1-7.84 Å20 Å2-0 Å2
2---4.68 Å20 Å2
3----3.16 Å2
Refinement stepCycle: 1 / Resolution: 2.66→24.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5196 0 101 92 5389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135440
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174856
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.6627389
X-RAY DIFFRACTIONr_angle_other_deg1.2331.58111257
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8965625
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.87522.056321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.40415906
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5291538
X-RAY DIFFRACTIONr_chiral_restr0.0710.2696
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026036
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021240
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_it4.7775.5842509
X-RAY DIFFRACTIONr_mcbond_other4.7755.5832508
X-RAY DIFFRACTIONr_mcangle_it7.0988.3713131
X-RAY DIFFRACTIONr_mcangle_other7.0988.3723132
X-RAY DIFFRACTIONr_scbond_it4.8336.0742931
X-RAY DIFFRACTIONr_scbond_other4.8326.0762932
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4568.9514259
X-RAY DIFFRACTIONr_long_range_B_refined10.39565.36311
X-RAY DIFFRACTIONr_long_range_B_other10.39665.3066310
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.66→2.69 Å
RfactorNum. reflection% reflection
Rfree0.358 61 -
Rwork0.293 1137 -
obs--82.17 %

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