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- PDB-5f5n: The structure of monooxygenase KstA11 in complex with NAD and its... -

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Basic information

Entry
Database: PDB / ID: 5f5n
TitleThe structure of monooxygenase KstA11 in complex with NAD and its substrate
ComponentsMonooxygenase
KeywordsOXIDOREDUCTASE / monooxygenase / complex / 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
Chem-5VD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Monooxygenase
Similarity search - Component
Biological speciesMicromonospora sp. TP-A0468 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.304 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 1.3Nov 8, 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: Monooxygenase
B: Monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,98319
Polymers61,4052
Non-polymers3,57717
Water18,7721042
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-2 kcal/mol
Surface area22760 Å2
Unit cell
Length a, b, c (Å)56.476, 66.025, 176.319
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Monooxygenase


Mass: 30702.682 Da / Num. of mol.: 2 / Fragment: UNP residues 5-293
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

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Non-polymers , 6 types, 1059 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-5VD / methyl (1~{R},2~{R},4~{S})-2-methyl-2,4,5,7,10-pentakis(oxidanyl)-6,11-bis(oxidanylidene)-3,4-dihydro-1~{H}-tetracene-1-carboxylate


Mass: 414.362 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H18O9
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1042 / 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: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Magnesium chloride hexahydrate,HEPES, Polyacrylic acid sodium salt 5100

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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: Nov 16, 2014
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 159744 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 10.55 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.037 / Rrim(I) all: 0.092 / Χ2: 3.354 / Net I/av σ(I): 44.75 / Net I/σ(I): 12.3 / Num. measured all: 1063765
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.3-1.326.80.38679490.9290.1610.4192.13999.9
1.32-1.356.90.3579470.9360.1450.382.273100
1.35-1.376.90.31379610.950.130.342.373100
1.37-1.470.28478820.9550.1170.3082.442100
1.4-1.4370.25379330.9620.1050.2742.511100
1.43-1.466.90.22179560.9680.0920.242.74100
1.46-1.56.90.19179120.9760.080.2072.922100
1.5-1.546.90.16979610.980.0710.1843.04899.9
1.54-1.596.90.15479340.9830.0650.1683.158100
1.59-1.646.80.1479730.9850.0590.1523.247100
1.64-1.76.80.12879670.9880.0540.1393.364100
1.7-1.766.80.11780120.9890.0490.1273.488100
1.76-1.846.80.10479480.9910.0440.1133.639100
1.84-1.946.70.09880260.9920.0420.1073.85199.9
1.94-2.066.50.09180090.9920.0390.0994.19599.9
2.06-2.226.30.08580270.9930.0370.0934.45399.8
2.22-2.456.20.08280620.9940.0360.094.53399.7
2.45-2.86.20.07780910.9930.0340.0844.599.7
2.8-3.5360.06981240.9940.0310.0754.61399.2
3.53-505.90.06380700.9930.0290.074.31694.7

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.15data extraction
HKL-2000data processing
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F5L

5f5l


Resolution: 1.304→31.105 Å / FOM work R set: 0.8879 / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1657 7998 5.02 %
Rwork0.1435 151466 -
obs0.1446 159464 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.75 Å2 / Biso mean: 18.68 Å2 / Biso min: 5.55 Å2
Refinement stepCycle: final / Resolution: 1.304→31.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4332 0 239 1042 5613
Biso mean--23.29 31.34 -
Num. residues----578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064833
X-RAY DIFFRACTIONf_angle_d1.1946643
X-RAY DIFFRACTIONf_chiral_restr0.077740
X-RAY DIFFRACTIONf_plane_restr0.006848
X-RAY DIFFRACTIONf_dihedral_angle_d13.0591750
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3043-1.31910.19952080.16894403461186
1.3191-1.33460.20932730.1649645237100
1.3346-1.35090.2092550.153750305285100
1.3509-1.3680.19522750.148150245299100
1.368-1.3860.18012510.134450185269100
1.386-1.4050.17012610.130550825343100
1.405-1.4250.18312590.13550345293100
1.425-1.44630.18292610.137650525313100
1.4463-1.46890.16992640.132550515315100
1.4689-1.4930.1652690.125250405309100
1.493-1.51870.152630.117650235286100
1.5187-1.54630.15142460.120150695315100
1.5463-1.57610.15292430.121450845327100
1.5761-1.60820.15072960.123450425338100
1.6082-1.64320.16472440.124450535297100
1.6432-1.68140.16822780.123150545332100
1.6814-1.72350.1682520.128550795331100
1.7235-1.77010.15822610.133751235384100
1.7701-1.82220.17712520.135950835335100
1.8222-1.8810.15212930.131150385331100
1.881-1.94820.15832790.137351125391100
1.9482-2.02620.15342950.141750485343100
2.0262-2.11840.16382740.145750915365100
2.1184-2.230.17172680.139950945362100
2.23-2.36970.1612880.147651095397100
2.3697-2.55260.16652640.15751515415100
2.5526-2.80930.18362780.151551305408100
2.8093-3.21550.16412490.15475158540799
3.2155-4.04970.15392850.14325137542298
4.0497-31.11410.16863140.16455090540494

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