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- PDB-5f5l: The structure of monooxygenase KstA11 in the biosynthetic pathway... -

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Basic information

Entry
Database: PDB / ID: 5f5l
TitleThe structure of monooxygenase KstA11 in the biosynthetic pathway of kosinostatin
ComponentsMonooxygenase
KeywordsOXIDOREDUCTASE / monooxygenase / dearomatization / kosinostatin
Function / homology
Function and homology information


monooxygenase activity / nucleotide binding
Similarity search - Function
: / NmrA-like domain / NmrA-like family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Monooxygenase
Similarity search - Component
Biological speciesMicromonospora sp. TP-A0468 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.68 Å
AuthorsPan, L. / Gong, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Basic Research Program of China2013CB836900 China
a Shanghai Rising Star Scholar award13QA1404300 China
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Hydroxyl regioisomerization of anthracycline catalyzed by a four-enzyme cascade
Authors: Zhang, Z. / Gong, Y.-K. / Zhou, Q. / Hu, Y. / Ma, H.-M. / Chen, Y.-S. / Igarashi, Y. / Pan, L. / Tang, G.-L.
History
DepositionDec 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Mar 1, 2017Group: Database references
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6397
Polymers31,0241
Non-polymers6156
Water5,711317
1
A: Monooxygenase
hetero molecules

A: Monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,27814
Polymers62,0482
Non-polymers1,22912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Unit cell
Length a, b, c (Å)93.748, 93.748, 71.182
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Monooxygenase


Mass: 31024.229 Da / Num. of mol.: 1 / Fragment: UNP residues 4-293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora sp. TP-A0468 (bacteria) / Plasmid: pET37b
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: A0A023GUL3
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: DL-Malic acid, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 26, 2014
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 39067 / % possible obs: 100 % / Redundancy: 28.4 % / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.02 / Rrim(I) all: 0.103 / Χ2: 2.565 / Net I/av σ(I): 65.5 / Net I/σ(I): 10 / Num. measured all: 1107719
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.65-1.6828.719070.9150.2171.206100
1.68-1.7128.719420.9470.1821.2271000.9610.978
1.71-1.7428.819000.9550.1481.2751000.7850.799
1.74-1.7828.819370.9730.1331.2681000.7030.716
1.78-1.8228.819260.9760.1081.3281000.5750.585
1.82-1.8628.918930.990.0851.3561000.4480.456
1.86-1.928.819370.9880.0721.4581000.380.386
1.9-1.9628.919240.9910.0641.661000.3420.348
1.96-2.0128.919350.9960.0471.6061000.2520.256
2.01-2.0828.819330.9950.0421.891000.2220.226
2.08-2.1528.919390.9980.0321.8451000.1680.171
2.15-2.2428.819400.9980.0281.9311000.1480.15
2.24-2.3428.819330.9980.0252.3331000.1350.137
2.34-2.4628.719560.9980.0222.5541000.1190.121
2.46-2.6228.519630.9980.0223.2381000.1140.116
2.62-2.822819530.9980.0214.3081000.1070.109
2.82-3.1127.419860.9990.0195.0821000.0960.098
3.11-3.5527.319890.9990.0144.9181000.0730.075
3.55-4.4826.920260.9990.0114.8311000.0560.057
4.48-5026.121480.9960.0116.12799.60.0570.058

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data processing
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.68→39.18 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.226 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1769 1838 5 %RANDOM
Rwork0.1288 ---
obs0.1312 34902 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 136.42 Å2 / Biso mean: 26.589 Å2 / Biso min: 10.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20 Å2
2--0.71 Å2-0 Å2
3----1.42 Å2
Refinement stepCycle: final / Resolution: 1.68→39.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2168 0 38 317 2523
Biso mean--43.31 37.62 -
Num. residues----290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192290
X-RAY DIFFRACTIONr_bond_other_d0.0010.022185
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.9633123
X-RAY DIFFRACTIONr_angle_other_deg0.74834987
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3385301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.22721.7100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.56615310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8211527
X-RAY DIFFRACTIONr_chiral_restr0.1050.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212633
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02550
X-RAY DIFFRACTIONr_rigid_bond_restr8.59134475
X-RAY DIFFRACTIONr_sphericity_free25.45578
X-RAY DIFFRACTIONr_sphericity_bonded14.36354664
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.204 141 -
Rwork0.129 2522 -
all-2663 -
obs--100 %

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