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- PDB-6ow0: Crystal structure of mithramycin 3-side chain keto-reductase MtmW... -

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Basic information

Entry
Database: PDB / ID: 6ow0
TitleCrystal structure of mithramycin 3-side chain keto-reductase MtmW in complex with NAD+ and PEG
ComponentsMtmW
KeywordsOXIDOREDUCTASE / Natural product / Biosynthesis / Aureolic acid / Reductase
Function / homology
Function and homology information


Potassium channel, voltage-dependent, beta subunit, KCNAB-related / NADP-dependent oxidoreductase domain / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / DI(HYDROXYETHYL)ETHER / Putative side chain reductase
Similarity search - Component
Biological speciesStreptomyces argillaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsHou, C. / Yu, X. / Rohr, J. / Tsodikov, O.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM105977-01A1 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Discovery of a Cryptic Intermediate in Late Steps of Mithramycin Biosynthesis.
Authors: Wheeler, R. / Yu, X. / Hou, C. / Mitra, P. / Chen, J.M. / Herkules, F. / Ivanov, D.N. / Tsodikov, O.V. / Rohr, J.
History
DepositionMay 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MtmW
B: MtmW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4527
Polymers72,6752
Non-polymers1,7775
Water2,018112
1
A: MtmW
hetero molecules

A: MtmW
hetero molecules

A: MtmW
hetero molecules

A: MtmW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,11616
Polymers145,3494
Non-polymers3,76612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_665-y+1,x+1,z1
crystal symmetry operation4_465y-1,-x+1,z1
Buried area13930 Å2
ΔGint-27 kcal/mol
Surface area47230 Å2
MethodPISA
2
B: MtmW
hetero molecules

B: MtmW
hetero molecules

B: MtmW
hetero molecules

B: MtmW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,69112
Polymers145,3494
Non-polymers3,3428
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area12360 Å2
ΔGint-57 kcal/mol
Surface area46320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.679, 124.679, 107.359
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422
DetailsAs per the authors gel filtration cannot exclude a possibility of an octamer

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Components

#1: Protein MtmW


Mass: 36337.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces argillaceus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q194Q1*PLUS
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.87 Å3/Da / Density % sol: 57.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 19% PEG400, 0.1 M Hepes, 7.0, 0.2 M CaCl2.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 24728 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.066 / Net I/σ(I): 15.4
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.809 / Num. unique obs: 1208 / Rpim(I) all: 0.329 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OVX

6ovx


Resolution: 2.67→35 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.921 / SU B: 11.842 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.591 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22848 1296 5.3 %RANDOM
Rwork0.18075 ---
obs0.18332 23344 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.359 Å2
Baniso -1Baniso -2Baniso -3
1--2.54 Å20 Å20 Å2
2---2.54 Å20 Å2
3---5.08 Å2
Refinement stepCycle: 1 / Resolution: 2.67→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4750 0 114 112 4976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134960
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174681
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.6716751
X-RAY DIFFRACTIONr_angle_other_deg1.2121.58510777
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5355620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.89720.079253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35915789
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6681550
X-RAY DIFFRACTIONr_chiral_restr0.0590.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025530
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021082
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_it2.4474.2172492
X-RAY DIFFRACTIONr_mcbond_other2.444.2162491
X-RAY DIFFRACTIONr_mcangle_it3.9726.3193108
X-RAY DIFFRACTIONr_mcangle_other3.9726.3213109
X-RAY DIFFRACTIONr_scbond_it3.0834.742468
X-RAY DIFFRACTIONr_scbond_other3.0824.7412469
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0986.9753644
X-RAY DIFFRACTIONr_long_range_B_refined7.01449.5965202
X-RAY DIFFRACTIONr_long_range_B_other7.00449.595194
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.67→2.739 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 81 -
Rwork0.273 1691 -
obs--100 %

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