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- PDB-2ovb: Crystal Structure of StaL-sulfate complex -

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Basic information

Entry
Database: PDB / ID: 2ovb
TitleCrystal Structure of StaL-sulfate complex
ComponentsStaL
KeywordsStructural Genomics / Unknown Function / StaL sulfate complex / sulfotransferase / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology
Function and homology information


desulfo-A47934 sulfotransferase / sulfation / sulfotransferase activity / antibiotic biosynthetic process / cytoplasm
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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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 / MOLECULAR REPLACEMENT / Resolution: 2.61 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
Revision 1.4Aug 30, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: StaL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4994
Polymers32,2111
Non-polymers2883
Water59433
1
A: StaL
hetero molecules

A: StaL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9978
Polymers64,4212
Non-polymers5766
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)88.733, 88.733, 169.691
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.9958.89
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2951vapor diffusion, hanging drop5.50.1M Bis-Tris pH5.5,0.2M Ammonium Sulfate, 22% PEG 3350, vapor diffusion, hanging drop, temperature 295K
2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDOct 2, 2005mirrors
2
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1siliconeSINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.61→50 Å / Num. obs: 12609 / % possible obs: 99.3 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.051 / Χ2: 0.959 / Net I/σ(I): 22.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.61-2.76.40.32511430.7421,293.4
2.7-2.819.40.25512160.8091,299.9
2.81-2.9411.20.17612360.891,2100
2.94-3.0911.60.13212421.0051,2100
3.09-3.2911.60.08612470.9961,2100
3.29-3.5411.60.06312540.9961,2100
3.54-3.911.50.051126411,299.9
3.9-4.4611.20.04112781.0011,299.8
4.46-5.6210.90.04413041.0041,299.8
5.62-509.70.03814251.0041,299.6

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Phasing

Phasing MRRfactor: 0.442 / Cor.coef. Fo:Fc: 0.64
Highest resolutionLowest resolution
Rotation3 Å45.55 Å
Translation3 Å45.55 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OV8

2ov8


Resolution: 2.61→76.92 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.873 / SU B: 20.595 / SU ML: 0.219 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.415 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.269 612 4.9 %RANDOM
Rwork0.228 ---
obs0.23 12554 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.929 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å2-0.39 Å20 Å2
2---0.79 Å20 Å2
3---1.18 Å2
Refinement stepCycle: LAST / Resolution: 2.61→76.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 0 15 33 1946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211957
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.9612661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3815246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.24922.89283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.43415302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.2491515
X-RAY DIFFRACTIONr_chiral_restr0.0780.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021493
X-RAY DIFFRACTIONr_nbd_refined0.2110.2874
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21316
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.292
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.24
X-RAY DIFFRACTIONr_mcbond_it0.6741.51267
X-RAY DIFFRACTIONr_mcangle_it1.05821959
X-RAY DIFFRACTIONr_scbond_it1.363812
X-RAY DIFFRACTIONr_scangle_it2.1924.5702
LS refinement shellResolution: 2.61→2.678 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 39 -
Rwork0.298 779 -
obs-818 92.95 %
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)
11.15280.01530.2380.83780.01681.14520.01760.03430.0624-0.0108-0.0639-0.09930.10710.11480.0464-0.02360.0239-0.0666-0.04720.05360.053817.24664.37544.2996
21.6803-0.6950.34662.0313-1.09512.98790.0095-0.45070.39910.2589-0.0871-0.1557-0.2413-0.04210.07760.0506-0.0115-0.1496-0.0352-0.12570.065314.099778.886561.3469
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 - 131109 - 149
42236 - 269254 - 287

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