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- PDB-3kg1: Crystal structure of SnoaB, a cofactor-independent oxygenase from... -

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Basic information

Entry
Database: PDB / ID: 3kg1
TitleCrystal structure of SnoaB, a cofactor-independent oxygenase from Streptomyces nogalater, mutant N63A
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: 2.5 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 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.3Feb 21, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)43,0065
Polymers42,9353
Non-polymers712
Water61334
1
C: SnoaB
hetero molecules

A: SnoaB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6954
Polymers28,6242
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3170 Å2
ΔGint-28 kcal/mol
Surface area10210 Å2
MethodPISA
2
B: SnoaB

B: SnoaB


Theoretical massNumber of molelcules
Total (without water)28,6242
Polymers28,6242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area2830 Å2
ΔGint-14 kcal/mol
Surface area10510 Å2
MethodPISA
3
C: SnoaB
hetero molecules

A: SnoaB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6954
Polymers28,6242
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)57.831, 111.603, 48.087
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUARGARGAA13 - 5523 - 65
21GLUGLUARGARGBB13 - 5523 - 65
31GLUGLUARGARGCC13 - 5523 - 65
12SERSERALAALAAA60 - 10270 - 112
22SERSERALAALABB60 - 10270 - 112
32SERSERALAALACC60 - 10270 - 112

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Components

#1: Protein SnoaB


Mass: 14311.804 Da / Num. of mol.: 3 / Fragment: oxygenase / Mutation: N63A
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 1.98 Å3/Da / Density % sol: 31.94 %
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: 2.5→30 Å / Num. all: 11301 / Num. obs: 11301 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 52.5 Å2 / Rsym value: 0.103 / Net I/σ(I): 13.2
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2 / Num. unique all: 1591 / Rsym value: 0.571 / % possible all: 99.3

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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: 2.5→29.42 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.904 / Occupancy max: 1 / Occupancy min: 0 / SU B: 25.621 / SU ML: 0.261 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.71 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.261 568 5 %RANDOM
Rwork0.206 ---
all0.209 11271 --
obs0.209 11271 99.87 %-
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: 70.71 Å2 / Biso mean: 35.709 Å2 / Biso min: 17.85 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å20 Å20 Å2
2---2.91 Å20 Å2
3---4.57 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 2 34 2371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212385
X-RAY DIFFRACTIONr_bond_other_d0.0010.021610
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.9073250
X-RAY DIFFRACTIONr_angle_other_deg0.90133827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2935297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.21621.694124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.16415328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1571526
X-RAY DIFFRACTIONr_chiral_restr0.0790.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212751
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02592
X-RAY DIFFRACTIONr_mcbond_it0.4661.51478
X-RAY DIFFRACTIONr_mcbond_other0.1051.5587
X-RAY DIFFRACTIONr_mcangle_it0.90422360
X-RAY DIFFRACTIONr_scbond_it1.4343907
X-RAY DIFFRACTIONr_scangle_it2.4734.5888
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1100 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
AMEDIUM POSITIONAL0.610.5
BMEDIUM POSITIONAL0.550.5
CMEDIUM POSITIONAL0.640.5
AMEDIUM THERMAL0.472
BMEDIUM THERMAL0.452
CMEDIUM THERMAL0.492
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 35 -
Rwork0.296 749 -
all-784 -
obs--98.25 %
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)
13.65150.2608-1.20371.1589-0.06032.60210.0129-0.24720.04580.18670.0062-0.2343-0.02580.1352-0.01920.10660.0232-0.04940.029-0.01050.05178.426-12.69610.381
24.56110.0032-1.56412.7187-1.11892.93110.06060.46280.1576-0.2269-0.12790.1488-0.2345-0.0420.06730.12870.0333-0.04260.10340.01250.030720.5725.66630.768
32.3113-0.7371-0.48723.40990.54631.3331-0.0916-0.01590.07380.08590.12260.0847-0.06560.0924-0.0310.0389-0.0161-0.00720.03690.00750.009510.2616.2343.317
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 107
2X-RAY DIFFRACTION2B11 - 108
3X-RAY DIFFRACTION3C10 - 106

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