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

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Basic information

Entry
Database: PDB / ID: 3kng
TitleCrystal structure of SnoaB, a cofactor-independent oxygenase from Streptomyces nogalater, determined to 1.9 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: 1.9 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
DepositionNov 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: SnoaB
B: SnoaB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,58611
Polymers27,9452
Non-polymers6419
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-40 kcal/mol
Surface area10420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.681, 82.681, 83.417
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-125-

SO4

21B-125-

SO4

31A-207-

HOH

41B-142-

HOH

51B-187-

HOH

61B-205-

HOH

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Components

#1: Protein SnoaB


Mass: 13972.412 Da / Num. of mol.: 2
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: (NH4)2SO4, NaCl, Na-cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→58.7 Å / Num. all: 23455 / Num. obs: 23455 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.8 % / Biso Wilson estimate: 22.1 Å2 / Rsym value: 0.095 / Net I/σ(I): 19.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 15.2 % / Mean I/σ(I) obs: 6.5 / Num. unique all: 3344 / Rsym value: 0.441 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
MxCuBEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1lq9

1lq9


Resolution: 1.9→19.64 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY. RESIDUAL DENSITY FOR A LIGAND IN THE ACTIVE SITE WAS NOT MODELLED, BECAUSE THE CHEMICAL NATURE OF THIS COMPOUND IS UNKNOWN.
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1168 5 %RANDOM
Rwork0.186 ---
all0.188 23371 --
obs0.188 23371 99.99 %-
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: 73.56 Å2 / Biso mean: 27.608 Å2 / Biso min: 13.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1643 0 34 163 1840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0211716
X-RAY DIFFRACTIONr_angle_refined_deg1.0031.9222354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7455222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.14521.6392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60715249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1761521
X-RAY DIFFRACTIONr_chiral_restr0.0680.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211363
X-RAY DIFFRACTIONr_mcbond_it1.3931.51022
X-RAY DIFFRACTIONr_mcangle_it2.32121662
X-RAY DIFFRACTIONr_scbond_it3.5533694
X-RAY DIFFRACTIONr_scangle_it5.2594.5678
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 79 -
Rwork0.2 1612 -
all-1691 -
obs-3344 100 %
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)
14.8116-4.3506-2.745111.24753.31451.70820.01940.0802-0.26790.0474-0.0988-0.1644-0.0381-0.10680.07940.0763-0.00140.02070.1178-0.00670.122326.412.569-11.816
21.1813-0.37920.28461.64620.49290.4319-0.15620.0739-0.0088-0.07880.113-0.0672-0.08180.04010.04310.0939-0.03450.02330.1148-0.02150.087829.82925.798-14.115
34.889-0.2912.21493.86022.25142.5631-0.46670.00070.4478-0.18250.11680.2559-0.2572-0.01210.34990.1685-0.0644-0.06230.13050.04820.126115.28827.214-16.516
41.34050.23430.48691.30680.66390.4485-0.09070.0334-0.13850.01090.1386-0.0761-0.03150.0579-0.04790.07790.00240.01970.1151-0.00690.109331.26120.57-9.104
51.2135-0.0251-0.48472.5966-0.23241.39970.0350.0926-0.3564-0.16440.0006-0.46430.04160.0404-0.03550.07030.0280.02890.1154-0.02420.238121.086.304-15.185
60.18070.43280.85274.2681-2.753111.614-0.11150.010.0149-0.1114-0.1205-0.1244-0.2070.20840.23190.1647-0.0184-0.02520.1250.03350.08312.81618.009-18.292
70.89380.210.10230.4454-0.54052.0795-0.03970.0905-0.1186-0.08860.035-0.00570.07920.06620.00470.1118-0.01320.00150.0884-0.01420.08759.4694.684-16.534
86.0764-0.0658-0.16691.4935-0.81666.0097-0.0662-0.3765-0.4641-0.057-0.0211-0.3453-0.01160.29860.08720.05450.0147-0.00560.10650.04950.149921.0925.514-7.37
90.76020.36750.22990.4715-0.20160.5329-0.06880.0789-0.0022-0.07180.01420.0359-0.00250.02770.05460.1067-0.0091-0.0160.1035-0.00260.07685.85411.009-16.68
102.54011.6242-0.12531.4299-0.32741.1991-0.19940.19150.0998-0.21270.23990.08480.08670.0458-0.04040.1481-0.019-0.00420.11920.00830.053619.20222.161-19.049
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 19
2X-RAY DIFFRACTION2A20 - 49
3X-RAY DIFFRACTION3A50 - 58
4X-RAY DIFFRACTION4A59 - 96
5X-RAY DIFFRACTION5A97 - 108
6X-RAY DIFFRACTION6B11 - 19
7X-RAY DIFFRACTION7B20 - 49
8X-RAY DIFFRACTION8B50 - 58
9X-RAY DIFFRACTION9B59 - 95
10X-RAY DIFFRACTION10B96 - 108

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