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- PDB-4ilt: Structure of the dioxygenase domain of SACTE_2871, a novel dioxyg... -

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Basic information

Entry
Database: PDB / ID: 4ilt
TitleStructure of the dioxygenase domain of SACTE_2871, a novel dioxygenase carbohydrate-binding protein fusion from the cellulolytic bacterium Streptomyces sp. SirexAA-E
ComponentsIntradiol ring-cleavage dioxygenase
KeywordsOXIDOREDUCTASE / iron center / intradiol dioxygenase / carbohydrate binding domain
Function / homology
Function and homology information


oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / hydrolase activity, hydrolyzing O-glycosyl compounds / ferric iron binding / carbohydrate binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
Carbohydrate-binding module family 5/12 / Protocatechuate 3,4-Dioxygenase, subunit A / Aromatic compound dioxygenase / : / Intradiol ring-cleavage dioxygenase, C-terminal / Intradiol ring-cleavage dioxygenase, core / Dioxygenase / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 ...Carbohydrate-binding module family 5/12 / Protocatechuate 3,4-Dioxygenase, subunit A / Aromatic compound dioxygenase / : / Intradiol ring-cleavage dioxygenase, C-terminal / Intradiol ring-cleavage dioxygenase, core / Dioxygenase / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Intradiol ring-cleavage dioxygenase
Similarity search - Component
Biological speciesStreptomyces sp. SirexAA-E (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsBianchetti, C.M. / Takasuka, T.E. / Bergeman, L.F. / Harmann, C.H. / Fox, B.G.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Fusion of Dioxygenase and Lignin-binding Domains in a Novel Secreted Enzyme from Cellulolytic Streptomyces sp. SirexAA-E.
Authors: Bianchetti, C.M. / Harmann, C.H. / Takasuka, T.E. / Hura, G.L. / Dyer, K. / Fox, B.G.
History
DepositionDec 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Jul 10, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Intradiol ring-cleavage dioxygenase
B: Intradiol ring-cleavage dioxygenase
C: Intradiol ring-cleavage dioxygenase
D: Intradiol ring-cleavage dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,07310
Polymers66,7794
Non-polymers2946
Water3,567198
1
A: Intradiol ring-cleavage dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7863
Polymers16,6951
Non-polymers912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Intradiol ring-cleavage dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7512
Polymers16,6951
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Intradiol ring-cleavage dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7512
Polymers16,6951
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Intradiol ring-cleavage dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7863
Polymers16,6951
Non-polymers912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.192, 85.125, 70.264
Angle α, β, γ (deg.)90.000, 95.530, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Intradiol ring-cleavage dioxygenase


Mass: 16694.754 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. SirexAA-E (bacteria) / Gene: SACTE_2871 / Plasmid: PVP68K / Production host: Escherichia coli (E. coli) / References: UniProt: G2NEL6
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.19 Å3/Da / Density % sol: 43.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18% Polyethylene glycol 3350, 5mM CoCl2, 5mM NiCl2, 5mM CdCl2, 5mM MnCl2, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 8, 2012 / Details: mirrors and beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionRedundancy: 3.7 % / Av σ(I) over netI: 8.92 / Number: 69135 / Rmerge(I) obs: 0.155 / Χ2: 1.02 / D res high: 2.55 Å / D res low: 50 Å / Num. obs: 18549 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.925099.810.0661.1353.6
5.496.9210010.0881.0383.8
4.85.4910010.0971.2863.8
4.364.810010.0961.23.8
4.054.3610010.0991.1853.8
3.814.0510010.1161.233.8
3.623.8110010.1341.1763.8
3.463.6210010.1561.2033.8
3.333.4610010.1711.1743.8
3.213.3310010.1961.1943.7
3.113.2110010.2171.053.7
3.023.1110010.2631.0253.7
2.943.0210010.3150.9563.7
2.872.9499.810.3190.943.7
2.812.8710010.3580.8143.7
2.752.8110010.4960.8063.7
2.692.7510010.5040.7943.7
2.642.6910010.5520.7333.7
2.592.6410010.6460.7453.7
2.552.5999.210.6510.7383.6
ReflectionResolution: 2.55→50 Å / Num. obs: 18549 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.155 / Χ2: 1.025 / Net I/σ(I): 4.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.55-2.593.60.6519090.738199.2
2.59-2.643.70.6469140.7451100
2.64-2.693.70.5529270.7331100
2.69-2.753.70.5049070.7941100
2.75-2.813.70.4969490.8061100
2.81-2.873.70.3589300.8141100
2.87-2.943.70.3199030.94199.8
2.94-3.023.70.3159280.9561100
3.02-3.113.70.2639161.0251100
3.11-3.213.70.2179231.051100
3.21-3.333.70.1969331.1941100
3.33-3.463.80.1719241.1741100
3.46-3.623.80.1569131.2031100
3.62-3.813.80.1349441.1761100
3.81-4.053.80.1169331.231100
4.05-4.363.80.0999191.1851100
4.36-4.83.80.0969351.21100
4.8-5.493.80.0979361.2861100
5.49-6.923.80.0889461.0381100
6.92-503.60.0669601.135199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.55 Å42.56 Å
Translation2.55 Å42.56 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→42.562 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.35 / σ(F): 1.38 / Phase error: 29.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2681 930 5.02 %
Rwork0.2033 --
obs0.2066 18519 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.4 Å2 / Biso mean: 36.7184 Å2 / Biso min: 16.47 Å2
Refinement stepCycle: LAST / Resolution: 2.55→42.562 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4695 0 6 198 4899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014845
X-RAY DIFFRACTIONf_angle_d1.3016621
X-RAY DIFFRACTIONf_chiral_restr0.074717
X-RAY DIFFRACTIONf_plane_restr0.008885
X-RAY DIFFRACTIONf_dihedral_angle_d13.8931747
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.55-2.68950.33961240.25572278240290
2.6895-2.8580.37531320.25725242656100
2.858-3.07860.32131360.244325602696100
3.0786-3.38830.28151320.222425272659100
3.3883-3.87830.28281350.195125502685100
3.8783-4.88510.22631340.168925542688100
4.8851-42.56840.20541370.180925962733100

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