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- PDB-3kg0: Crystal structure of SnoaB, a cofactor-independent oxygenase from... -

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Basic information

Entry
Database: PDB / ID: 3kg0
TitleCrystal structure of SnoaB, a cofactor-independent oxygenase from Streptomyces nogalater, determined to 1.7 resolution
ComponentsSnoaB
KeywordsOXIDOREDUCTASE / polyketide / anthracycline / oxygenase / cofactor-independent
Function / homology
Function and homology information


deoxynogalonate monooxygenase / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of one atom of oxygen (internal monooxygenases or internal mixed function oxidases) / antibiotic biosynthetic process
Similarity search - Function
ABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Deoxynogalonate monooxygenase
Similarity search - Component
Biological speciesStreptomyces nogalater (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsKoskiniemi, H. / Grocholski, T. / Lindqvist, Y. / Mantsala, P. / Niemi, J. / Schneider, G.
Citation
Journal: Biochemistry / Year: 2010
Title: Crystal structure of the cofactor-independent monooxygenase SnoaB from Streptomyces nogalater: implications for the reaction mechanism
Authors: Grocholski, T. / Koskiniemi, H. / Lindqvist, Y. / Mantsala, P. / Niemi, J. / Schneider, G.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Expression, purification and crystallization of the cofactor-independent monooxygenase SnoaB from the nogalamycin biosynthetic pathway
Authors: Koskiniemi, H. / Grocholski, T. / Schneider, G. / Niemi, J.
History
DepositionOct 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SnoaB
B: SnoaB
C: SnoaB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3579
Polymers43,0643
Non-polymers2936
Water3,531196
1
A: SnoaB
hetero molecules

C: SnoaB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8695
Polymers28,7102
Non-polymers1603
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area2800 Å2
ΔGint-11 kcal/mol
Surface area10050 Å2
MethodPISA
2
B: SnoaB
hetero molecules

B: SnoaB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9768
Polymers28,7102
Non-polymers2666
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area2660 Å2
ΔGint-12 kcal/mol
Surface area10430 Å2
MethodPISA
3
C: SnoaB
hetero molecules

A: SnoaB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8695
Polymers28,7102
Non-polymers1603
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)58.262, 112.383, 47.127
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein SnoaB


Mass: 14354.829 Da / Num. of mol.: 3 / Fragment: oxygenase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces nogalater (bacteria) / Gene: SnoaB / Plasmid: modified from pBAD/HisB / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: O54259
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT G25A IS IN FACT THE NATIVE SEQUENCE. THEY CONFIRMED THEIR NATIVE SEQUENCE BY DNA- ...AUTHORS STATE THAT G25A IS IN FACT THE NATIVE SEQUENCE. THEY CONFIRMED THEIR NATIVE SEQUENCE BY DNA-SEQUENCING THREE TIMES. THIS HAS BEEN NOTED IN THE SECONDARY REFERENCE, KOSKINIEMI ET AL. 2009

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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: 1.97 Å3/Da / Density % sol: 31.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG MME 2K, KBr, pentaerythritol ethoxylate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 12, 2009
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 32939 / Num. obs: 32939 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 23.9 Å2 / Rsym value: 0.035 / Net I/σ(I): 24.8
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 3585 / Rsym value: 0.354 / % possible all: 73.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.5.0070refinement
PDB_EXTRACT3.005data extraction
MxCuBEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→40 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0 / SU B: 4.674 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1614 4.9 %RANDOM
Rwork0.174 ---
all0.176 32936 --
obs0.176 32936 94.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 59.14 Å2 / Biso mean: 20.141 Å2 / Biso min: 3.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2---0.88 Å20 Å2
3---0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 15 196 2546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212437
X-RAY DIFFRACTIONr_bond_other_d0.0010.021637
X-RAY DIFFRACTIONr_angle_refined_deg1.3281.913331
X-RAY DIFFRACTIONr_angle_other_deg0.87733911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2135308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.27221.783129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5315339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7021527
X-RAY DIFFRACTIONr_chiral_restr0.0910.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212802
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02602
X-RAY DIFFRACTIONr_mcbond_it1.23621487
X-RAY DIFFRACTIONr_mcbond_other0.352589
X-RAY DIFFRACTIONr_mcangle_it2.13832395
X-RAY DIFFRACTIONr_scbond_it2.9174950
X-RAY DIFFRACTIONr_scangle_it4.475926
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 84 -
Rwork0.245 1607 -
all-1691 -
obs--66.55 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.2660.8026-6.02092.2448-0.408814.59510.1344-0.19390.0732-0.0893-0.04480.0664-0.254-0.1901-0.08960.04550.0308-0.02560.0462-0.02280.02621.428-10.127-10.253
21.4814-0.1292-1.22311.61810.18253.7636-0.0286-0.23530.08450.02760.1123-0.35030.24020.2644-0.08380.03630.0207-0.02140.0624-0.02910.103713.413-16.067-13.235
34.50240.58430.29684.74621.04337.3279-0.05910.3417-0.0878-0.26820.1934-0.16770.06830.1626-0.13420.04510.00630.00680.0496-0.03170.05585.815-18.299-23.253
46.87150.6340.38590.0847-0.02050.16030.1423-0.25850.27560.0841-0.06160.0422-0.12970.0241-0.08060.207-0.0210.00990.2137-0.0630.14999.426-8.224-2.885
53.0981-0.331-0.62610.06490.2872.6311-0.0683-0.24740.2129-0.03050.0199-0.0487-0.3026-0.05010.04830.1430.04110.00030.0642-0.05340.14035.861-9.617-14.013
611.14194.7959-6.02276.9094-5.91826.16040.06540.35140.05830.0313-0.07770.1234-0.1883-0.00340.01220.0791-0.0103-0.00650.0556-0.00270.031923.5724.86810.326
74.5946-1.7087-0.32913.7384-1.33573.63170.13690.6376-0.2745-0.3291-0.22150.4372-0.1318-0.23520.08470.09430.0363-0.07890.1689-0.05030.080216.7761.9384.656
84.5774-1.1841-0.75082.7901-1.68823.1440.1580.59740.4837-0.0353-0.1994-0.0273-0.5899-0.1950.04140.24420.0508-0.04560.1550.04950.096118.7711.2966.521
913.4396-0.15044.41923.938-0.12634.7197-0.26280.1085-0.1022-0.08190.19930.1617-0.3746-0.01460.06350.04830.00870.00420.02390.01260.026913.534.36316.506
1010.4099-3.3707-5.98744.61793.16926.53780.24950.30760.6912-0.2805-0.1606-0.3314-0.137-0.0235-0.0890.06130.00760.02990.08960.06190.098334.2555.075.565
114.1432-4.5494-0.358611.4770.63790.9655-0.01830.0805-0.043-0.1817-0.04480.49890.03850.03990.06320.02920.02370.0010.04290.02350.04365.39816.265-22.684
122.66371.0168-0.292613.7346-0.7581.168-0.0993-0.12330.0142-0.06690.1287-0.19080.05940.2043-0.02930.02790.0414-0.00060.10210.00250.0118.30312.949-16.68
131.52221.2052-1.3554.9158-1.16211.4187-0.1484-0.24520.02360.19150.09460.0430.09160.27350.05380.07560.04070.00450.10680.04530.05578.63316.536-16.499
142.1201-1.4737-0.53710.1110.3210.2386-0.0853-0.12060.2022-0.24580.1766-0.2626-0.04290.1063-0.09140.1-0.0190.03520.0845-0.03170.042416.97718.269-26.556
157.0528-5.0154-2.96675.37691.62973.35740.05750.223-0.0409-0.0055-0.15060.1488-0.0607-0.13510.09320.01710.00750.01080.01760.01880.062-2.06119.245-21.654
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 19
2X-RAY DIFFRACTION2A20 - 48
3X-RAY DIFFRACTION3A49 - 64
4X-RAY DIFFRACTION4A65 - 82
5X-RAY DIFFRACTION5A83 - 107
6X-RAY DIFFRACTION6B11 - 24
7X-RAY DIFFRACTION7B25 - 58
8X-RAY DIFFRACTION8B59 - 89
9X-RAY DIFFRACTION9B90 - 95
10X-RAY DIFFRACTION10B96 - 107
11X-RAY DIFFRACTION11C10 - 23
12X-RAY DIFFRACTION12C24 - 41
13X-RAY DIFFRACTION13C42 - 71
14X-RAY DIFFRACTION14C72 - 94
15X-RAY DIFFRACTION15C95 - 106

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