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- PDB-6jh7: Crystal structure of AerF from Microcystis aeruginosa -

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Basic information

Entry
Database: PDB / ID: 6jh7
TitleCrystal structure of 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
ACETATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Short chain dehydrogenase family protein
Similarity search - Component
Biological speciesMicrocystis aeruginosa DIANCHI905 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 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)60,9985
Polymers60,6832
Non-polymers3153
Water9,026501
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)121,99710
Polymers121,3664
Non-polymers6316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area12090 Å2
ΔGint-83 kcal/mol
Surface area37560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.581, 101.581, 116.094
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-517-

HOH

21A-568-

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-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Calcium Chloride, 0.1 M HEPES sodium pH 7.0, 23% (v/v) polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97907 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.38→45 Å / Num. obs: 122470 / % possible obs: 98.5 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.023 / Net I/σ(I): 33.9
Reflection shellResolution: 1.38→1.4 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.906 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 5628 / Rpim(I) all: 0.301 / % possible all: 92.1

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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: 3U49

3u49


Resolution: 1.38→45 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.335 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.047 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16639 6158 5 %RANDOM
Rwork0.14146 ---
obs0.14272 116265 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.757 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0 Å2
2---0.06 Å2-0 Å2
3---0.12 Å2
Refinement stepCycle: 1 / Resolution: 1.38→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3852 0 13 501 4366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194307
X-RAY DIFFRACTIONr_bond_other_d0.0010.024299
X-RAY DIFFRACTIONr_angle_refined_deg1.1271.9745948
X-RAY DIFFRACTIONr_angle_other_deg0.72639950
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2335646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.58725.548155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70615789
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5441514
X-RAY DIFFRACTIONr_chiral_restr0.0640.2730
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025002
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02922
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_it1.6152.1432210
X-RAY DIFFRACTIONr_mcbond_other1.612.1422208
X-RAY DIFFRACTIONr_mcangle_it2.2093.2222789
X-RAY DIFFRACTIONr_mcangle_other2.2093.2232790
X-RAY DIFFRACTIONr_scbond_it1.8842.3342097
X-RAY DIFFRACTIONr_scbond_other1.8842.3342098
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4113.4143090
X-RAY DIFFRACTIONr_long_range_B_refined3.64819.1765523
X-RAY DIFFRACTIONr_long_range_B_other3.64819.1785524
X-RAY DIFFRACTIONr_rigid_bond_restr0.84338602
X-RAY DIFFRACTIONr_sphericity_free28.8985144
X-RAY DIFFRACTIONr_sphericity_bonded12.04858869
LS refinement shellResolution: 1.381→1.417 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 423 -
Rwork0.198 8071 -
obs--93.49 %

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