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- PDB-5thq: Comprehensive Analysis of a Novel Ketoreductase for Pentangular P... -

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Basic information

Entry
Database: PDB / ID: 5thq
TitleComprehensive Analysis of a Novel Ketoreductase for Pentangular Polyphenol Biosynthesis
Components3-oxoacyl-ACP reductase3-oxoacyl-(acyl-carrier-protein) reductase
KeywordsOXIDOREDUCTASE / Arixanthomycin / Pentangular polyphenol Polyketide / Ketoreduction
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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 / 3-oxoacyl-ACP reductase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsValentic, T.R. / Tsai, S.C. / Brady, S.F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM100305 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM076330 United States
CitationJournal: ACS Chem. Biol. / Year: 2016
Title: Comprehensive Analysis of a Novel Ketoreductase for Pentangular Polyphenol Biosynthesis.
Authors: Valentic, T.R. / Jackson, D.R. / Brady, S.F. / Tsai, S.C.
History
DepositionSep 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: 3-oxoacyl-ACP reductase
B: 3-oxoacyl-ACP reductase
C: 3-oxoacyl-ACP reductase
F: 3-oxoacyl-ACP reductase
A: 3-oxoacyl-ACP reductase
E: 3-oxoacyl-ACP reductase
H: 3-oxoacyl-ACP reductase
D: 3-oxoacyl-ACP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,44316
Polymers232,4808
Non-polymers5,9638
Water8,989499
1
G: 3-oxoacyl-ACP reductase
B: 3-oxoacyl-ACP reductase
C: 3-oxoacyl-ACP reductase
F: 3-oxoacyl-ACP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,2228
Polymers116,2404
Non-polymers2,9824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18400 Å2
ΔGint-71 kcal/mol
Surface area33750 Å2
MethodPISA
2
A: 3-oxoacyl-ACP reductase
E: 3-oxoacyl-ACP reductase
H: 3-oxoacyl-ACP reductase
D: 3-oxoacyl-ACP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,2228
Polymers116,2404
Non-polymers2,9824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18550 Å2
ΔGint-76 kcal/mol
Surface area33950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.340, 86.540, 106.970
Angle α, β, γ (deg.)90.00, 108.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
3-oxoacyl-ACP reductase / 3-oxoacyl-(acyl-carrier-protein) reductase


Mass: 29059.971 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: arx21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A023PKG5
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 1.99 Å3/Da / Density % sol: 38.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Sodium Acetate and 30-32% PEG 4,000 / Temp details: (Room temperature in Irvine CA)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→86.54 Å / Num. obs: 79685 / % possible obs: 98.3 % / Redundancy: 6.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.122 / Net I/σ(I): 10.6
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.663 / Mean I/σ(I) obs: 3.8 / CC1/2: 0.932 / % possible all: 95.3

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Apo ARX 21

Resolution: 2.3→86.305 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2166 1990 2.5 %
Rwork0.1687 --
obs0.1699 79632 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→86.305 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14966 0 384 499 15849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115622
X-RAY DIFFRACTIONf_angle_d1.2521242
X-RAY DIFFRACTIONf_dihedral_angle_d21.5775586
X-RAY DIFFRACTIONf_chiral_restr0.0752474
X-RAY DIFFRACTIONf_plane_restr0.0082690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35750.25441330.18595343X-RAY DIFFRACTION96
2.3575-2.42130.28411420.19545391X-RAY DIFFRACTION96
2.4213-2.49250.26441360.20115384X-RAY DIFFRACTION96
2.4925-2.5730.23441420.18725454X-RAY DIFFRACTION97
2.573-2.6650.27461390.19065415X-RAY DIFFRACTION97
2.665-2.77170.24641430.19215467X-RAY DIFFRACTION97
2.7717-2.89780.25171440.18835564X-RAY DIFFRACTION98
2.8978-3.05060.24761430.19145574X-RAY DIFFRACTION99
3.0506-3.24180.21671400.18315627X-RAY DIFFRACTION100
3.2418-3.49210.23151450.17745653X-RAY DIFFRACTION100
3.4921-3.84350.19421440.15675651X-RAY DIFFRACTION100
3.8435-4.39960.17741450.14565653X-RAY DIFFRACTION100
4.3996-5.54290.18881430.14135689X-RAY DIFFRACTION100
5.5429-86.36540.18961510.15395777X-RAY DIFFRACTION100

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