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

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Basic information

Entry
Database: PDB / ID: 6ovq
TitleCrystal structure of mithramycin 3-side chain keto-reductase MtmW
ComponentsPutative Side chain reductase
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
Putative side chain reductase
Similarity search - Component
Biological speciesStreptomyces argillaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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

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Assembly

Deposited unit
A: Putative Side chain reductase
B: Putative Side chain reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8594
Polymers72,6752
Non-polymers1842
Water6,738374
1
A: Putative Side chain reductase
hetero molecules

A: Putative Side chain reductase
hetero molecules

A: Putative Side chain reductase
hetero molecules

A: Putative Side chain reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,7188
Polymers145,3494
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area7460 Å2
ΔGint-39 kcal/mol
Surface area44980 Å2
MethodPISA
2
B: Putative Side chain reductase
hetero molecules

B: Putative Side chain reductase
hetero molecules

B: Putative Side chain reductase
hetero molecules

B: Putative Side chain reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,7188
Polymers145,3494
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area7190 Å2
ΔGint-25 kcal/mol
Surface area44020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.105, 131.105, 79.769
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
DetailsSize-exclusion indicates tetramer or octamer, PISA analysis indicates tetramer

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Components

#1: Protein Putative Side chain reductase


Mass: 36337.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces argillaceus (bacteria) / Gene: mtmW / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q194Q1*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 374 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMtmW sequence corresponds to the GenBank accession code MK907881

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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: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 14% w/v PEG1500, 0.1 M Na-Citrate, pH 6.0

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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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 61625 / % possible obs: 97.5 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 29
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.675 / Num. unique obs: 3022 / % possible all: 95.5

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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: 3ERP

3erp


Resolution: 1.8→33 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.662 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.114 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21276 3115 5.1 %RANDOM
Rwork0.18443 ---
obs0.18589 57992 97.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.012 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å20 Å2
2---0.74 Å20 Å2
3---1.48 Å2
Refinement stepCycle: 1 / Resolution: 1.8→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4456 0 12 374 4842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0134546
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174374
X-RAY DIFFRACTIONr_angle_refined_deg1.2641.6366162
X-RAY DIFFRACTIONr_angle_other_deg1.2421.57110056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1415579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.80819.833239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36215749
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.831549
X-RAY DIFFRACTIONr_chiral_restr0.0610.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025111
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02996
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_it1.5263.1012336
X-RAY DIFFRACTIONr_mcbond_other1.5233.12335
X-RAY DIFFRACTIONr_mcangle_it2.4094.6342908
X-RAY DIFFRACTIONr_mcangle_other2.4094.6352909
X-RAY DIFFRACTIONr_scbond_it1.973.4422210
X-RAY DIFFRACTIONr_scbond_other1.973.4422211
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2235.0513255
X-RAY DIFFRACTIONr_long_range_B_refined4.92937.1494959
X-RAY DIFFRACTIONr_long_range_B_other4.77536.7894887
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 223 -
Rwork0.237 4307 -
obs--98.39 %

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