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- PDB-6jhb: Crystal structure of NADPH and 4-hydroxyphenylpyruvic acid bound ... -

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Basic information

Entry
Database: PDB / ID: 6jhb
TitleCrystal structure of NADPH and 4-hydroxyphenylpyruvic acid 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
3-(4-HYDROXY-PHENYL)PYRUVIC ACID / Chem-NDP / Short chain dehydrogenase family protein
Similarity search - Component
Biological speciesMicrocystis aeruginosa DIANCHI905 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsQiu, X. / Wei, Y. / Zhu, W.
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

Downloads & links

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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)62,3545
Polymers60,6832
Non-polymers1,6713
Water95553
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)124,70810
Polymers121,3664
Non-polymers3,3426
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area16650 Å2
ΔGint-92 kcal/mol
Surface area34150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.124, 101.124, 115.096
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ENO / 3-(4-HYDROXY-PHENYL)PYRUVIC ACID / HPP


Mass: 180.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop
Details: 0.2 M NaCl, 0.1 M Na HEPES pH7.5, 25 % (w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.91939 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91939 Å / Relative weight: 1
ReflectionResolution: 2.27→45 Å / Num. obs: 27238 / % possible obs: 96.2 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 17.957
Reflection shellResolution: 2.32→2.36 Å / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 5.474 / Num. unique obs: 1372

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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: 2.27→45 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.907 / SU B: 7.223 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.348 / ESU R Free: 0.247 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27044 1362 5.1 %RANDOM
Rwork0.2387 ---
obs0.24031 25509 95.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.053 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å2-0 Å20 Å2
2--0.14 Å20 Å2
3----0.28 Å2
Refinement stepCycle: 1 / Resolution: 2.27→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3692 0 109 53 3854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193881
X-RAY DIFFRACTIONr_bond_other_d0.0070.023672
X-RAY DIFFRACTIONr_angle_refined_deg1.5662.0015288
X-RAY DIFFRACTIONr_angle_other_deg0.92938426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7865505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.89825.263133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.08715631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8381516
X-RAY DIFFRACTIONr_chiral_restr0.0960.2632
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024362
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02825
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_it2.3874.3932012
X-RAY DIFFRACTIONr_mcbond_other2.3834.3912011
X-RAY DIFFRACTIONr_mcangle_it3.5086.5782509
X-RAY DIFFRACTIONr_mcangle_other3.5096.5792510
X-RAY DIFFRACTIONr_scbond_it2.5214.6231869
X-RAY DIFFRACTIONr_scbond_other2.524.6241870
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8426.8642775
X-RAY DIFFRACTIONr_long_range_B_refined5.68735.7634476
X-RAY DIFFRACTIONr_long_range_B_other5.68835.7634473
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.27→2.329 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 97 -
Rwork0.323 1795 -
obs--92.29 %

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