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- PDB-4dif: Structure of A1-type ketoreductase -

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Basic information

Entry
Database: PDB / ID: 4dif
TitleStructure of A1-type ketoreductase
ComponentsAmphB
KeywordsOXIDOREDUCTASE / ketoreductase / Rossmann Fold / NADP+
Function / homology
Function and homology information


macrolide biosynthetic process / DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / nucleotide binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / Polyketide synthase, docking domain / Erythronolide synthase docking domain / PKS_PP_betabranch / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension ...Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / Polyketide synthase, docking domain / Erythronolide synthase docking domain / PKS_PP_betabranch / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / PKS_KR / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Ketosynthase family 3 (KS3) domain profile. / 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 / Thiolase-like / Phosphopantetheine attachment site / 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
Biological speciesStreptomyces nodosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.521 Å
AuthorsZheng, J. / Keatinge-Clay, A.T.
CitationJournal: To be Published
Title: Structure and mutagenesis of A2-type ketoreductase from modular polyketide synthase reveals insights into stereospecificity
Authors: Zheng, J. / Keatinge-Clay, A.T.
History
DepositionJan 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AmphB
B: AmphB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,5405
Polymers102,9582
Non-polymers1,5833
Water11,043613
1
A: AmphB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2242
Polymers51,4791
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: AmphB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3163
Polymers51,4791
Non-polymers8382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.546, 63.716, 71.983
Angle α, β, γ (deg.)72.92, 67.22, 89.74
Int Tables number1
Space group name H-MP1
Detailsmonomer

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Components

#1: Protein AmphB


Mass: 51478.766 Da / Num. of mol.: 2 / Fragment: ketoreductase domain (UNP Residues 2529-3003) / Mutation: G355T, Q364H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces nodosus (bacteria) / Strain: Streptomyces nodosus / Gene: amphB / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q93NW7, 3-oxoacyl-[acyl-carrier-protein] reductase
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 613 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.75
Details: 3.1 M ammonium sulfate, 200 mM NaCl, 100 mM sodium cacodylate, pH 6.75, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.213 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 10, 2011
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.213 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. all: 146711 / Num. obs: 127786 / % possible obs: 87.1 % / Observed criterion σ(F): 8.2 / Observed criterion σ(I): 8.2 / Redundancy: 1.9 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 14.9
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.124 / Mean I/σ(I) obs: 8.2 / Num. unique all: 6093 / % possible all: 83.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MJS

3mjs


Resolution: 1.521→50 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.917 / SU B: 2.248 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 6435 5 %RANDOM
Rwork0.19838 ---
obs0.19967 121327 86.94 %-
all-127762 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.192 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.15 Å2-0.24 Å2
2---0.43 Å2-0.5 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.521→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6938 0 102 613 7653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197194
X-RAY DIFFRACTIONr_angle_refined_deg1.0231.9779844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8795950
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.90122.867286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.394151018
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.21564
X-RAY DIFFRACTIONr_chiral_restr0.2210.21140
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.0215504
LS refinement shellResolution: 1.521→1.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 421 -
Rwork0.221 8806 -
obs-8806 85.05 %
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)
10.0125-0.0086-0.01810.16150.04690.0862-0.00030.0089-0.00440.0126-0.0032-0.0122-0.0073-0.00260.00350.003-0.0012-0.00210.01420.0030.011-10.22992.1644-17.1884
20.02250.00810.0070.13440.04340.0712-0.0035-0.01010.0035-0.0103-0.00050.00090.00670.00020.00410.00360.00350.00190.01260.00360.0116-13.1462-16.532123.8453
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 473
2X-RAY DIFFRACTION1A501
3X-RAY DIFFRACTION2B-2 - 473
4X-RAY DIFFRACTION2B501 - 502

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