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- PDB-3woh: Structure of Ketoreductase SiaM from Streptomyces sp. A7248 -

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Basic information

Entry
Database: PDB / ID: 3woh
TitleStructure of Ketoreductase SiaM from Streptomyces sp. A7248
ComponentsSiaM
KeywordsOXIDOREDUCTASE / enzyme / tetramer / ketoreductase / ACP / Reduction
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid biosynthetic process / NAD binding
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase / : / PKS_KR / 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-oxoacyl-(acyl-carrier-protein) reductase / : / PKS_KR / 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
3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Component
Biological speciesStreptomyces (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWang, H. / Zhang, H.
CitationJournal: Plos One / Year: 2014
Title: Structural insight into the tetramerization of an iterative ketoreductase siam through aromatic residues in the interfaces
Authors: Wang, H. / Zhang, H. / Zou, Y. / Mi, Y. / Lin, S. / Xie, Z. / Yan, Y. / Zhang, H.
History
DepositionDec 29, 2013Deposition site: PDBJ / Processing site: PDBJ
SupersessionAug 6, 2014ID: 4HSY
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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

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Assembly

Deposited unit
A: SiaM


Theoretical massNumber of molelcules
Total (without water)26,0781
Polymers26,0781
Non-polymers00
Water27015
1
A: SiaM

A: SiaM

A: SiaM

A: SiaM


Theoretical massNumber of molelcules
Total (without water)104,3114
Polymers104,3114
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation7_645y+1,x-1,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area12460 Å2
ΔGint-81 kcal/mol
Surface area32510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.425, 56.425, 122.838
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein SiaM


Mass: 26077.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces (bacteria) / Strain: A7248 / Production host: Escherichia coli (E. coli) / References: UniProt: K9M8L2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 1.89 Å3/Da / Density % sol: 34.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.5M Ammonium sulfate, 0.1M Tris, 12%(v/v) Glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→51.274 Å / Num. all: 7354 / Num. obs: 7354 / % possible obs: 75 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9 % / Biso Wilson estimate: 46.72 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2UVD

2uvd


Resolution: 2.5→51.274 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7203 / SU ML: 0.29 / σ(F): 1.35 / Phase error: 30.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2707 341 4.64 %RANDOM
Rwork0.2174 ---
obs0.22 7349 99.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.09 Å2 / Biso mean: 67.4637 Å2 / Biso min: 26.11 Å2
Refinement stepCycle: LAST / Resolution: 2.5→51.274 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1707 0 0 15 1722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061724
X-RAY DIFFRACTIONf_angle_d1.1422324
X-RAY DIFFRACTIONf_chiral_restr0.037272
X-RAY DIFFRACTIONf_plane_restr0.003306
X-RAY DIFFRACTIONf_dihedral_angle_d15.084628
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-3.14970.34741610.274134253586100
3.1497-51.28510.24831800.1993583376399
Refinement TLS params.Method: refined / Origin x: 18.6926 Å / Origin y: -16.2395 Å / Origin z: -15.4302 Å
111213212223313233
T0.3369 Å20.0541 Å2-0.0919 Å2-0.558 Å20.0525 Å2--0.4086 Å2
L2.6928 °2-0.59 °2-0.0066 °2-2.2445 °2-0.1389 °2--3.1004 °2
S-0.123 Å °0.7325 Å °0.431 Å °-0.2929 Å °-0.17 Å °0.2406 Å °-0.5254 Å °-0.5662 Å °0.2332 Å °
Refinement TLS groupSelection details: ALL

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