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- PDB-3mjv: Structure of A-type Ketoreductases from Modular Polyketide Synthase -

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Basic information

Entry
Database: PDB / ID: 3mjv
TitleStructure of A-type Ketoreductases from Modular Polyketide Synthase
ComponentsAmphB
KeywordsOXIDOREDUCTASE / Rossmann fold
Function / homology
Function and homology information


macrolide biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / nucleotide binding / identical protein binding
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, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding ...Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / Polyketide synthase, docking domain / Erythronolide synthase docking domain / PKS_PP_betabranch / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / 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: 1.46 Å
AuthorsZheng, J. / Taylor, C.A. / Piasecki, S.K. / Keatinge-Clay, A.T.
CitationJournal: Structure / Year: 2010
Title: Structural and Functional Analysis of A-Type Ketoreductases from the Amphotericin Modular Polyketide Synthase.
Authors: Zheng, J. / Taylor, C.A. / Piasecki, S.K. / Keatinge-Clay, A.T.
History
DepositionApr 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AmphB
B: AmphB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2624
Polymers102,7712
Non-polymers1,4912
Water9,602533
1
A: AmphB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1312
Polymers51,3861
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: AmphB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1312
Polymers51,3861
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.502, 63.691, 71.920
Angle α, β, γ (deg.)72.93, 67.21, 89.76
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain: (Details: A)

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Components

#1: Protein AmphB


Mass: 51385.660 Da / Num. of mol.: 2 / Fragment: ketoreductase domain / Mutation: W359F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces nodosus (bacteria) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / 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: 48.69 %
Crystal growTemperature: 293 K / pH: 6.75
Details: 3.1 M ammonium sulfate, 200 mM NaCl, 100 mM sodium cacodylate, pH 6.75, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2009
RadiationMonochromator: DOUBLE FLAT CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 1.46→62.89 Å / Num. obs: 137417 / % possible obs: 83.2 % / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 19.9
Reflection shellResolution: 1.46→1.49 Å / Redundancy: 2 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 1.9 / % possible all: 91.9

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Processing

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

3mje


Resolution: 1.46→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.262 / SU ML: 0.056 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.236 6885 5 %RANDOM
Rwork0.199 ---
obs0.201 137417 82.9 %-
all-86965 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20.3 Å2-0.13 Å2
2---0.67 Å2-0.55 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.46→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6918 0 96 533 7547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0217157
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3571.9799792
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4135949
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26922.982285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.589151017
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5551563
X-RAY DIFFRACTIONr_chiral_restr0.220.21133
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0215485
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.4961.54699
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.327394
X-RAY DIFFRACTIONr_scbond_it3.5132458
X-RAY DIFFRACTIONr_scangle_it5.1514.52398
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3436 / Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0 Å

Auth asym-IDTypeWeight position
Amedium positional0.5
Bmedium thermal2
LS refinement shellResolution: 1.46→1.5 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 278 -
Rwork0.321 10075 -
obs--86.83 %
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)
10.0407-0.0103-0.01770.26610.06890.142-0.00260.0159-0.00540.0217-0.0011-0.0114-0.01370.0010.00370.005-0.0026-0.0020.0113-0.00040.0112-10.19591.9382-17.3124
20.0465-0.01610.01010.22770.08520.1299-0.0045-0.01430.0024-0.01570.00110.00340.0104-0.00090.00340.00680.00150.00380.00870.00020.0131-13.0448-16.511523.9709
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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