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- PDB-6jha: Crystal structure of NADPH bound AerF from Microcystis aeruginosa -

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Basic information

Entry
Database: PDB / ID: 6jha
TitleCrystal structure of NADPH bound AerF from Microcystis aeruginosa
ComponentsShort chain dehydrogenase family protein
KeywordsBIOSYNTHETIC PROTEIN / reductase
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / TRIETHYLENE GLYCOL / Short chain dehydrogenase family protein
Similarity search - Component
Biological speciesMicrocystis aeruginosa DIANCHI905 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsQiu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31400683 China
CitationJournal: J.Struct.Biol. / Year: 2019
Title: Structural and functional investigation of AerF, a NADPH-dependent alkenal double bond reductase participating in the biosynthesis of Choi moiety of aeruginosin
Authors: Qiu, X. / Wei, Y. / Zhu, W. / Fu, J. / Duan, X. / Jin, H. / Zhu, P. / Zhou, C. / Yan, X.
History
DepositionFeb 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Short chain dehydrogenase family protein
B: Short chain dehydrogenase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4746
Polymers60,6832
Non-polymers1,7914
Water4,648258
1
A: Short chain dehydrogenase family protein
B: Short chain dehydrogenase family protein
hetero molecules

A: Short chain dehydrogenase family protein
B: Short chain dehydrogenase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,94912
Polymers121,3664
Non-polymers3,5828
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area17500 Å2
ΔGint-90 kcal/mol
Surface area35370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.625, 101.625, 115.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-468-

HOH

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Components

#1: Protein Short chain dehydrogenase family protein / AerF


Mass: 30341.568 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microcystis aeruginosa DIANCHI905 (bacteria)
Gene: aerF, C789_498 / Production host: Escherichia coli (E. coli) / References: UniProt: L8NWH6
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 50.01 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Na HEPES pH7.5, 25 % (w/v) PEG2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 57850 / % possible obs: 98.8 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 35.451
Reflection shellResolution: 1.78→1.81 Å / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 3.165 / Num. unique obs: 2872 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JH7

6jh7


Resolution: 1.78→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.51 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23094 2877 5 %RANDOM
Rwork0.18915 ---
obs0.19118 54164 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.518 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å2-0 Å2
2--0.09 Å2-0 Å2
3----0.18 Å2
Refinement stepCycle: 1 / Resolution: 1.78→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3757 0 104 258 4119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194016
X-RAY DIFFRACTIONr_bond_other_d0.0020.023867
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.9995483
X-RAY DIFFRACTIONr_angle_other_deg0.87638887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8965531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.77725.6150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64915682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.931515
X-RAY DIFFRACTIONr_chiral_restr0.10.2654
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024536
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02860
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_it2.2232.8312046
X-RAY DIFFRACTIONr_mcbond_other2.2172.832045
X-RAY DIFFRACTIONr_mcangle_it3.0664.2252556
X-RAY DIFFRACTIONr_mcangle_other3.0664.2262557
X-RAY DIFFRACTIONr_scbond_it2.9323.1791969
X-RAY DIFFRACTIONr_scbond_other2.9323.1791969
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4584.642911
X-RAY DIFFRACTIONr_long_range_B_refined6.16623.7864727
X-RAY DIFFRACTIONr_long_range_B_other6.16623.7874727
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.781→1.827 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 188 -
Rwork0.281 3995 -
obs--98.63 %

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