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- PDB-3sju: Hedamycin Polyketide Ketoreductase bound to NADPH -

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Basic information

Entry
Database: PDB / ID: 3sju
TitleHedamycin Polyketide Ketoreductase bound to NADPH
ComponentsKeto reductase
KeywordsOXIDOREDUCTASE / short-chain dehydrogenase / reductase / Rossmann Fold / Type II Polyketide Ketoreductase
Function / homology
Function and homology information


monocarboxylic acid metabolic process / lipid metabolic process / oxidoreductase activity / nucleotide binding
Similarity search - Function
: / short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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 / Keto reductase
Similarity search - Component
Biological speciesStreptomyces griseoruber (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsJavidpour, P. / Tsai, S.-C.
CitationJournal: Biochemistry / Year: 2011
Title: Structural and Biochemical Studies of the Hedamycin Type II Polyketide Ketoreductase (HedKR): Molecular Basis of Stereo- and Regiospecificities.
Authors: Javidpour, P. / Das, A. / Khosla, C. / Tsai, S.C.
History
DepositionJun 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Keto reductase
B: Keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4104
Polymers57,9192
Non-polymers1,4912
Water68538
1
A: Keto reductase
B: Keto reductase
hetero molecules

A: Keto reductase
B: Keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,8198
Polymers115,8384
Non-polymers2,9824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area17190 Å2
ΔGint-79 kcal/mol
Surface area33320 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-26 kcal/mol
Surface area19550 Å2
MethodPISA
3
A: Keto reductase
hetero molecules

B: Keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4104
Polymers57,9192
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area5080 Å2
ΔGint-24 kcal/mol
Surface area20170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.698, 57.392, 82.106
Angle α, β, γ (deg.)90.000, 131.610, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Keto reductase


Mass: 28959.408 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseoruber (bacteria) / Gene: hedA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q67G28
#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.: 38 / 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

Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1 M imidazole pH 6.2, 50% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 15891 / % possible obs: 99.6 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.085 / Χ2: 1.195 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.39-2.486.30.23515350.992196.7
2.48-2.576.90.215601.103199.5
2.57-2.697.20.19115891.211100
2.69-2.837.40.15815711.2991100
2.83-3.017.50.13215941.2071100
3.01-3.247.50.11315811.2491100
3.24-3.577.50.09616071.1651100
3.57-4.097.40.08315981.1271100
4.09-5.157.30.06916011.2711100
5.15-507.20.05516551.2761100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 46.59 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.95 Å
Translation2.5 Å47.95 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.2629 / WRfactor Rwork: 0.1919 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8166 / SU B: 9.241 / SU ML: 0.219 / SU Rfree: 0.3066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2482 790 5 %RANDOM
Rwork0.1823 ---
obs0.1855 15868 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 110.39 Å2 / Biso mean: 48.407 Å2 / Biso min: 24.54 Å2
Baniso -1Baniso -2Baniso -3
1--3.78 Å20 Å2-0.6 Å2
2--4.07 Å20 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3696 0 96 38 3830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213860
X-RAY DIFFRACTIONr_angle_refined_deg1.7691.9695266
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9225508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42422.987154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.84215548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6561532
X-RAY DIFFRACTIONr_chiral_restr0.1190.2604
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022930
X-RAY DIFFRACTIONr_mcbond_it0.8591.52490
X-RAY DIFFRACTIONr_mcangle_it1.5823942
X-RAY DIFFRACTIONr_scbond_it2.33531370
X-RAY DIFFRACTIONr_scangle_it3.7434.51324
LS refinement shellResolution: 2.402→2.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 59 -
Rwork0.208 968 -
all-1027 -
obs--88.99 %

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