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

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Basic information

Entry
Database: PDB / ID: 6ovx
TitleCrystal structure of mithramycin 3-side chain keto-reductase MtmW in complex with NAD+, P422 form
ComponentsPutative side chain reductase
KeywordsOXIDOREDUCTASE / Natural product / Biosynthesis / Aureolic acid / Reductase
Function / homologyNADP-dependent oxidoreductase domain / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Putative side chain reductase
Function and homology information
Biological speciesStreptomyces argillaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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)74,3466
Polymers72,6752
Non-polymers1,6714
Water2,810156
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)148,69112
Polymers145,3494
Non-polymers3,3428
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 area12460 Å2
ΔGint-43 kcal/mol
Surface area43450 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)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 area9500 Å2
ΔGint-51 kcal/mol
Surface area45980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.479, 124.479, 107.066
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422
DetailsSize-exclusion indicates a tetramer or an 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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


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


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


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.85 Å3/Da / Density % sol: 56.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1mM NADP+ (with protein), reservoir: 16% PEG 1500, 0.1M 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: 2.1→50 Å / Num. obs: 49578 / % possible obs: 99.9 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 23.7
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 9 % / Rmerge(I) obs: 0.673 / Num. unique obs: 2406 / % possible all: 99.4

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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: 6OVQ

6ovq


Resolution: 2.1→35 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.967 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.159 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2321 2489 5.1 %RANDOM
Rwork0.20486 ---
obs0.20622 46759 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.802 Å2
Baniso -1Baniso -2Baniso -3
1--2.48 Å20 Å20 Å2
2---2.48 Å20 Å2
3---4.96 Å2
Refinement stepCycle: 1 / Resolution: 2.1→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4540 0 77 156 4773
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0134699
X-RAY DIFFRACTIONr_bond_other_d0.0030.0174454
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.6586386
X-RAY DIFFRACTIONr_angle_other_deg1.2441.58210247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4215589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.46120.247243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.38815762
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9591547
X-RAY DIFFRACTIONr_chiral_restr0.0590.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025237
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021021
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_it1.8493.9792374
X-RAY DIFFRACTIONr_mcbond_other1.8493.9782373
X-RAY DIFFRACTIONr_mcangle_it2.8215.9512957
X-RAY DIFFRACTIONr_mcangle_other2.825.9532958
X-RAY DIFFRACTIONr_scbond_it2.3554.4452325
X-RAY DIFFRACTIONr_scbond_other2.3554.4452326
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7566.5653430
X-RAY DIFFRACTIONr_long_range_B_refined5.2147.1315028
X-RAY DIFFRACTIONr_long_range_B_other5.18347.0965008
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 166 -
Rwork0.25 3217 -
obs--94.39 %

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