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- PDB-2gex: Crystal structure of SnoaL2 a putative hydroxylase from Streptomy... -

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Basic information

Entry
Database: PDB / ID: 2gex
TitleCrystal structure of SnoaL2 a putative hydroxylase from Streptomyces nogalater
ComponentsSnoL
KeywordsOXIDOREDUCTASE / alpha+beta barrel
Function / homologypolyketide metabolic process / SnoaL-like polyketide cyclase / Polyketide cyclase SnoaL-like / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / SnoL
Function and homology information
Biological speciesStreptomyces nogalater (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsBeinker, P. / Lohkamp, B. / Schneider, G.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal structures of SnoaL2 and AclR: two putative hydroxylases in the biosynthesis of aromatic polyketide antibiotics
Authors: Beinker, P. / Lohkamp, B. / Peltonen, T. / Niemi, J. / Mantsala, P. / Schneider, G.
History
DepositionMar 21, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SnoL
B: SnoL


Theoretical massNumber of molelcules
Total (without water)35,0602
Polymers35,0602
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.008, 90.008, 116.707
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein SnoL / SnoaL2 / putative hydroxylase


Mass: 17530.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces nogalater (bacteria) / Gene: snoal2 / Plasmid: pET30b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9RN64
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.89 Å3/Da / Density % sol: 68.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18-20% PEG 8000, 0.2M magnesium sulphate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.9790, 0.9788, 0.9823
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 20, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97881
30.98231
ReflectionResolution: 2.5→40 Å / Num. obs: 18909 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 64.4 Å2 / Rsym value: 0.082 / Net I/σ(I): 26.1
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 2417 / Rsym value: 0.605 / % possible all: 87.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→38.9 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.917 / SU B: 15.55 / SU ML: 0.166 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.281 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24892 964 5.1 %RANDOM
Rwork0.21794 ---
all0.21942 18058 --
obs0.21942 18058 98.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.14 Å20 Å2
2--0.29 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.5→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2212 0 0 31 2243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222302
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.9263142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2185291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6922.586116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.69415366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7861526
X-RAY DIFFRACTIONr_chiral_restr0.0880.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021798
X-RAY DIFFRACTIONr_nbd_refined0.2250.2923
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21553
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.280
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0670.214
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.21
X-RAY DIFFRACTIONr_mcbond_it0.9931.51444
X-RAY DIFFRACTIONr_mcangle_it1.26222279
X-RAY DIFFRACTIONr_scbond_it2.123990
X-RAY DIFFRACTIONr_scangle_it3.324.5856
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 69 -
Rwork0.336 1111 -
obs--84.35 %
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)
11.2586-1.2910.40032.0511-1.14153.4730.0838-0.2079-0.01340.17950.0935-0.1625-0.09220.0361-0.1773-0.1404-0.0157-0.0137-0.015-0.0677-0.095336.415630.366114.4642
22.90451.17380.63841.780.12181.9405-0.02260.6314-0.2796-0.31890.1336-0.05940.22310.1725-0.111-0.07060.0771-0.05040.0524-0.0966-0.067656.463323.209321.5184
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1472 - 147
2X-RAY DIFFRACTION2BB2 - 1342 - 134

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