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- PDB-2ipi: Crystal Structure of Aclacinomycin Oxidoreductase -

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Basic information

Entry
Database: PDB / ID: 2ipi
TitleCrystal Structure of Aclacinomycin Oxidoreductase
ComponentsAclacinomycin oxidoreductase (AknOx)
KeywordsOXIDOREDUCTASE / anthracycline / aclacinomycin / flavoenzyme / twinning / MAD
Function / homology
Function and homology information


aclacinomycin-N oxidase / aclacinomycin-A oxidase / antibiotic biosynthetic process / FAD binding / oxidoreductase activity
Similarity search - Function
Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Berberine/berberine-like / Berberine and berberine like / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. ...Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Berberine/berberine-like / Berberine and berberine like / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH-like superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
METHYL / FLAVIN-ADENINE DINUCLEOTIDE / Aclacinomycin-N/aclacinomycin-A oxidase
Similarity search - Component
Biological speciesStreptomyces galilaeus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsSultana, A. / Kursula, I. / Schneider, G. / Alexeev, I. / Niemi, J. / Mantsala, P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structure determination by multiwavelength anomalous diffraction of aclacinomycin oxidoreductase: indications of multidomain pseudomerohedral twinning.
Authors: Sultana, A. / Alexeev, I. / Kursula, I. / Mantsala, P. / Niemi, J. / Schneider, G.
History
DepositionOct 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aclacinomycin oxidoreductase (AknOx)
B: Aclacinomycin oxidoreductase (AknOx)
C: Aclacinomycin oxidoreductase (AknOx)
D: Aclacinomycin oxidoreductase (AknOx)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,8419
Polymers228,8874
Non-polymers3,9545
Water18,1771009
1
A: Aclacinomycin oxidoreductase (AknOx)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8193
Polymers57,2221
Non-polymers1,5972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aclacinomycin oxidoreductase (AknOx)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0072
Polymers57,2221
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Aclacinomycin oxidoreductase (AknOx)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0072
Polymers57,2221
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Aclacinomycin oxidoreductase (AknOx)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0072
Polymers57,2221
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.500, 266.200, 68.700
Angle α, β, γ (deg.)90.00, 119.00, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer.

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Components

#1: Protein
Aclacinomycin oxidoreductase (AknOx)


Mass: 57221.754 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces galilaeus (bacteria) / Gene: AknOx / Plasmid: pBADhisAknOx / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q0PCD7
#2: Chemical ChemComp-AKY / METHYL (2S,4R)-2-ETHYL-2,5,7-TRIHYDROXY-6,11-DIOXO-4-{[2,3,6-TRIDEOXY-4-O-{2,6-DIDEOXY-4-O-[(2S,6S)-6-METHYL-5-OXOTETRAHYDRO-2H-PYRAN-2-YL]-ALPHA-D-LYXO-HEXOPYRANOSYL}-3-(DIMETHYLAMINO)-D-RIBO-HEXOPYRANOSYL]OXY}-1,2,3,4,6,11-HEXAHYDROTETRACENE-1-CARBOXYLATE / ACLACINOMYCIN Y


Mass: 811.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H53NO15
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1009 / 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: 2.39 Å3/Da / Density % sol: 48.52 %
Crystal growTemperature: 293 K / pH: 8
Details: 20%(w/v)PEG6000, 0.2M ammonium chloride, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7B / Wavelength: 0.8423, 0.9793, 0.9797, 0.9392
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 24, 2006
RadiationMonochromator: SI [111], HORIZONTALLY FOCUSSING / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.84231
20.97931
30.97971
40.93921
ReflectionResolution: 1.65→20 Å / Num. obs: 246742 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 22.3 Å2 / Rsym value: 0.081 / Net I/σ(I): 11.5
Reflection shellResolution: 1.65→1.7 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.371 / % possible all: 57.3

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.9793.8-4.8
13 wavelength20.97970.5-8.3
13 wavelength30.93923.5-2.2
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se4.5790.3360.5010.1670.549
2Se26.8660.4550.4150.2070.993
3Se19.9660.3590.7780.1110.696
4Se23.3270.5440.1520.2820.784
5Se46.8150.9770.7340.1060.925
6Se50.5910.3990.6930.2290.862
7Se41.5620.6960.9510.4040.82
8Se54.7930.4240.8170.4290.998
9Se19.70.1140.2280.140.819
10Se47.5770.8590.9530.3120.909
11Se37.8630.1340.3760.1461.007
12Se38.0980.9140.0720.0040.864
13Se600.970.7420.2630.979
14Se45.9430.8770.740.4240.928
15Se47.6640.8440.540.1050.793
16Se26.3240.5710.6210.4790.71
17Se44.3040.9350.9540.3680.79
18Se600.6380.2350.4241.006
19Se31.6050.2970.9650.320.71
20Se59.7640.5410.9590.4110.976
21Se600.9880.4570.2041.086
22Se43.1280.2680.9590.3720.757
23Se49.0750.0650.2380.4990.637
24Se33.210.3290.4150.0760.475
Phasing dmFOM : 0.79 / FOM acentric: 0.79 / FOM centric: 0.78 / Reflection: 41882 / Reflection acentric: 41187 / Reflection centric: 695
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.6-19.9610.920.920.931663159469
5.4-8.60.880.880.8356095473136
4.3-5.40.880.890.8270546929125
3.8-4.30.860.860.8270976988109
3.2-3.80.780.780.761264812482166
3-3.20.550.550.517811772190

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Processing

Software
NameVersionClassificationNB
SOLVE2.09phasing
RESOLVE2.09phasing
REFMACrefinement
PDB_EXTRACT2data extraction
XDSdata reduction
XSCALEdata scaling
SHELXL-97refinement
RefinementMethod to determine structure: MAD / Resolution: 1.65→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE RWORK AND RFREE(RTWIN) MENTIONED HERE, ARE NOT THE VALUES OBTAINED FROM USUAL REFINEMENT PROCESS. THESE VALUES WERE OBTAINED AFTER USING THE TWIN PROTOCOL IN SHELXL DURING STRUCTURE ...Details: THE RWORK AND RFREE(RTWIN) MENTIONED HERE, ARE NOT THE VALUES OBTAINED FROM USUAL REFINEMENT PROCESS. THESE VALUES WERE OBTAINED AFTER USING THE TWIN PROTOCOL IN SHELXL DURING STRUCTURE REFINEMENT. SO, USUAL PROTOCOL FOR REFINEMENT WILL GIVE MUCH HIGHER VALUES FOR BOTH RWORK AND RTWIN COMPARED TO THE VALUES GIVEN IN THE TABLE HERE. The Rwork and Rfree are obtained from the twin refinement
RfactorNum. reflection% reflection
Rfree0.242 9545 -
obs0.185 -95.9 %
all-246723 -
Displacement parametersBiso mean: 18.009 Å2
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15310 0 270 1009 16589

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