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- PDB-2ov8: Crystal Structure of StaL -

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Basic information

Entry
Database: PDB / ID: 2ov8
TitleCrystal Structure of StaL
ComponentsStaL
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / StaL apoenzyme / sulfotransferase / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology
Function and homology information


desulfo-A47934 sulfotransferase / sulfotransferase activity / antibiotic biosynthetic process
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #460 / Sulfotransferase domain / Sulfotransferase domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Desulfo-A47934 sulfotransferase
Similarity search - Component
Biological speciesStreptomyces toyocaensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.58 Å
AuthorsShi, R. / Matte, A. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal structure of StaL, a glycopeptide antibiotic sulfotransferase from Streptomyces toyocaensis.
Authors: Shi, R. / Lamb, S.S. / Bhat, S. / Sulea, T. / Wright, G.D. / Matte, A. / Cygler, M.
History
DepositionFeb 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 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

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Assembly

Deposited unit
A: StaL


Theoretical massNumber of molelcules
Total (without water)32,2111
Polymers32,2111
Non-polymers00
Water23413
1
A: StaL

A: StaL


Theoretical massNumber of molelcules
Total (without water)64,4212
Polymers64,4212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Unit cell
Length a, b, c (Å)86.018, 86.018, 164.753
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
DetailsThe biological assembly is a dimer generated from monomer in the asymmetric unit by the operations: -x, y, 1/2-z

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Components

#1: Protein StaL


Mass: 32210.537 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces toyocaensis (bacteria) / Strain: NRRL 15009 / Gene: stal / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8KLM3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M NaAc pH4.6, 3.0M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X8C10.9795, 0.9794, 0.9643
SYNCHROTRONNSLS X2521
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDJun 9, 2005mirrors
ADSC QUANTUM 3152CCDAug 8, 2005mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1siliconeMADMx-ray1
2siliconeSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97941
30.96431
411
Reflection

D res low: 50 Å / Redundancy: 7 %

IDAv σ(I) over netINumberRmerge(I) obsΧ2D res high (Å)Num. obs% possible obs
121.51167330.03612.821659999.5
221.21169370.0330.992.821662499.5
323.51149790.03212.831636099.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.075094.710.0260.9996.6
4.826.0710010.0250.9997.1
4.214.8210010.02517.1
3.834.2110010.0317.1
3.553.8310010.04117.1
3.343.5510010.070.9997
3.183.3410010.1070.9997.1
3.043.1810010.1860.9997.1
2.923.0410010.3360.9937.1
2.822.9210010.4980.977.1
6.075095.520.0231.0016.7
4.826.0710020.0230.9997.1
4.214.8210020.0231.0017.1
3.834.2110020.0317.1
3.553.8310020.0410.9997.1
3.343.5510020.0720.9997
3.183.3410020.110.9997.1
3.043.1810020.1910.9927.1
2.923.0410020.3390.9587.1
2.822.9210020.5120.9657.1
6.09509630.020.9996.6
4.846.0910030.02117.1
4.234.8410030.02317.1
3.844.2310030.02917.1
3.573.8410030.04117.1
3.363.5710030.07317.1
3.193.3610030.1110.9997.1
3.053.1910030.191.0017.1
2.933.0510030.3520.9997.1
2.832.9310030.51417.1
ReflectionResolution: 2.58→50 Å / Num. obs: 12023 / % possible obs: 99.9 % / Redundancy: 29.7 % / Rmerge(I) obs: 0.055 / Χ2: 0.983 / Net I/σ(I): 20.7
Reflection shellResolution: 2.58→2.67 Å / Redundancy: 22.3 % / Rmerge(I) obs: 0.471 / Num. unique all: 1153 / Χ2: 0.978 / % possible all: 100

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 3 Å / D res low: 50 Å / FOM : 0.71 / Reflection: 7652
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97954.12-6.94
13 wavelength20.97952.15-7.72
13 wavelength30.9642.55-4.3
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.8910.1320.0821.429
2Se600.960.2280.0631.182
3Se600.7030.2150.0771.073
4Se600.3990.2910.0020.608
5Se600.3590.3180.030.954
6Se600.9820.2860.0390.829
7Se600.0280.6390.0510.56
Phasing MAD shell
Resolution (Å)FOM Reflection
10.79-500.6385
6.81-10.790.74676
5.33-6.810.83828
4.52-5.330.83981
3.99-4.520.791061
3.61-3.990.751164
3.33-3.610.641255
3.1-3.330.511302
Phasing dmFOM : 0.48 / FOM acentric: 0.47 / FOM centric: 0.53 / Reflection: 14229 / Reflection acentric: 11808 / Reflection centric: 2421
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.8-41.6890.980.980.97674406268
4.3-6.80.950.960.9119311478453
3.4-4.30.890.910.8123841958426
3-3.40.650.670.523882020368
2.6-30.140.140.1142663685581
2.4-2.60.040.040.0425862261325

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.09phasing
RESOLVE2.09phasing
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.58→74.54 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.929 / SU B: 24.523 / SU ML: 0.256 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.422 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.279 572 4.8 %RANDOM
Rwork0.249 ---
obs0.251 11969 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.811 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å2-0.47 Å20 Å2
2---0.93 Å20 Å2
3---1.4 Å2
Refinement stepCycle: LAST / Resolution: 2.58→74.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1768 0 0 13 1781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211812
X-RAY DIFFRACTIONr_angle_refined_deg1.481.9462470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2895238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94123.0366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.55815257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.538159
X-RAY DIFFRACTIONr_chiral_restr0.1060.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021376
X-RAY DIFFRACTIONr_nbd_refined0.2370.2888
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21243
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.287
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.23
X-RAY DIFFRACTIONr_mcbond_it0.6161.51217
X-RAY DIFFRACTIONr_mcangle_it1.07421876
X-RAY DIFFRACTIONr_scbond_it1.4963708
X-RAY DIFFRACTIONr_scangle_it2.3994.5594
LS refinement shellResolution: 2.579→2.646 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 40 -
Rwork0.3 809 -
obs-849 98.95 %
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)
15.8682-0.67791.6353.3598-0.46975.04720.0799-0.54160.04380.0236-0.01770.56670.4762-0.8852-0.0622-0.0594-0.121-0.1438-0.1395-0.0616-0.0392-17.085860.968739.3116
25.2941-2.3689-0.01054.828-1.74376.1261-0.04391.38441.7773-0.4586-0.3458-0.2867-0.6122-0.04840.38970.15670.0517-0.32630.07860.32670.4132-14.158474.21321.5451
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
113 - 9021 - 108
21132 - 216150 - 234
3291 - 103109 - 121
42110 - 131128 - 149
52237 - 269255 - 287

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