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- PDB-3qp9: The Structure of a C2-type Ketoreductase from a Modular Polyketid... -

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Basic information

Entry
Database: PDB / ID: 3qp9
TitleThe Structure of a C2-type Ketoreductase from a Modular Polyketide Synthase
ComponentsType I polyketide synthase PikAII
KeywordsOXIDOREDUCTASE / Rossmann Fold / ketoreductase / epimerization
Function / homology
Function and homology information


10-deoxymethynolide synthase / narbonolide synthase / macrolide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / phosphopantetheine binding / oxidoreductase activity / zinc ion binding
Similarity search - Function
Quinone oxidoreductase/zeta-crystallin, conserved site / : / Quinone oxidoreductase / zeta-crystallin signature. / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain ...Quinone oxidoreductase/zeta-crystallin, conserved site / : / Quinone oxidoreductase / zeta-crystallin signature. / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / GroES-like superfamily / Phosphopantetheine attachment site / Thiolase-like / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Narbonolide/10-deoxymethynolide synthase PikA2, modules 3 and 4
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsZheng, J. / Keatinge-Clay, A.T.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural and functional analysis of c2-type ketoreductases from modular polyketide synthases.
Authors: Zheng, J. / Keatinge-Clay, A.T.
History
DepositionFeb 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type I polyketide synthase PikAII
B: Type I polyketide synthase PikAII
C: Type I polyketide synthase PikAII
D: Type I polyketide synthase PikAII


Theoretical massNumber of molelcules
Total (without water)214,0184
Polymers214,0184
Non-polymers00
Water6,179343
1
A: Type I polyketide synthase PikAII


Theoretical massNumber of molelcules
Total (without water)53,5051
Polymers53,5051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Type I polyketide synthase PikAII


Theoretical massNumber of molelcules
Total (without water)53,5051
Polymers53,5051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Type I polyketide synthase PikAII


Theoretical massNumber of molelcules
Total (without water)53,5051
Polymers53,5051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Type I polyketide synthase PikAII


Theoretical massNumber of molelcules
Total (without water)53,5051
Polymers53,5051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.636, 150.088, 86.868
Angle α, β, γ (deg.)90.00, 105.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Type I polyketide synthase PikAII


Mass: 53504.555 Da / Num. of mol.: 4 / Fragment: UNP residues 920-1423
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces venezuelae (bacteria) / Strain: ATCC15439 / Gene: pikAII / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9ZGI4, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 33% PEG4000, 0.25 M sodium acetate, 0.1 M Tris-Cl, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 21, 2009
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. all: 151191 / Num. obs: 137509 / % possible obs: 90.95 % / Observed criterion σ(F): 2.7 / Observed criterion σ(I): 2.7 / Redundancy: 3.5 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 37
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 2.7 / Num. unique all: 9525 / % possible all: 86.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MJS

3mjs


Resolution: 1.88→31.23 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.921 / SU B: 10.435 / SU ML: 0.136 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27623 7250 5 %RANDOM
Rwork0.22676 ---
obs0.22924 137509 90.95 %-
all-151191 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.267 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å2-1.08 Å2
2--2.61 Å20 Å2
3----2.5 Å2
Refinement stepCycle: LAST / Resolution: 1.88→31.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13330 0 0 343 13673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02113603
X-RAY DIFFRACTIONr_angle_refined_deg2.0291.9618647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49851833
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.01822.198496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.057151857
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6615129
X-RAY DIFFRACTIONr_chiral_restr0.1620.22222
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02110383
X-RAY DIFFRACTIONr_mcbond_it1.2891.59162
X-RAY DIFFRACTIONr_mcangle_it2.1214464
X-RAY DIFFRACTIONr_scbond_it3.14934441
X-RAY DIFFRACTIONr_scangle_it4.5844.54183
LS refinement shellResolution: 1.88→1.93 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 511 -
Rwork0.392 9525 -
obs-9525 85.36 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.39150.13520.21750.09020.18370.53150.0287-0.04950.01280.0308-0.02690.0210.1456-0.0028-0.00190.1475-0.0259-0.01240.0371-0.00870.10298.9928-18.317727.0953
20.39980.3754-0.07680.4614-0.26210.4076-0.01430.03360.05120.03270.07110.073-0.0728-0.0193-0.05690.0567-0.00620.03850.0885-0.00160.126413.227612.093366.4617
30.5352-0.0566-0.11080.2738-0.24950.5070.1072-0.0907-0.0196-0.1071-0.10190.06490.02960.2323-0.00530.07970.0191-0.01990.18680.0050.0413-25.5841-2.765842.1372
40.78140.19190.46970.54320.1520.3696-0.03960.03310.08860.1739-0.0832-0.0303-0.0259-0.02380.12280.1179-0.0562-0.04070.08090.01020.09271.902817.96832.4442
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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