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- PDB-2ovf: Crystal Structure of StaL-PAP complex -

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Basic information

Entry
Database: PDB / ID: 2ovf
TitleCrystal Structure of StaL-PAP complex
ComponentsStaL
KeywordsStructural Genomics / Unknown Function / StaL-PAP 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / Desulfo-A47934 sulfotransferase
Similarity search - Component
Biological speciesStreptomyces toyocaensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 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

Downloads & links

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Assembly

Deposited unit
A: StaL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6382
Polymers32,2111
Non-polymers4271
Water21612
1
A: StaL
hetero molecules

A: StaL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2754
Polymers64,4212
Non-polymers8542
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)87.392, 87.392, 169.377
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: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.9 Å3/Da / Density % sol: 57.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris propane pH6.5,0.2M NaI, 18% PEG 3350, 10mM PAP, 5mM desulfo-A47934, vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 20, 2005 / Details: mirrors
RadiationMonochromator: silicone / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 8661 / % possible obs: 99.9 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.048 / Χ2: 1.001 / Net I/σ(I): 17.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.95-3.0611.20.5328251.0061100
3.06-3.1811.40.3248510.9991100
3.18-3.3211.10.2318341.0011100
3.32-3.511.50.1298531.0021100
3.5-3.7211.60.0818311.0011100
3.72-411.40.05186011100
4-4.4111.50.048590.9991100
4.41-5.0411.30.03387611100
5.04-6.35110.0389611100
6.35-509.80.0259760.999198.9

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Phasing

Phasing MRRfactor: 0.41 / Cor.coef. Fo:Fc: 0.737
Highest resolutionLowest resolution
Rotation3 Å45.25 Å
Translation3 Å45.25 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OV8

2ov8


Resolution: 2.95→76.92 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.872 / SU B: 30.409 / SU ML: 0.278 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.268 / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.269 418 4.9 %RANDOM
Rwork0.224 ---
obs0.226 8605 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.151 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.06 Å20 Å2
2---0.12 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.95→76.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1873 0 27 12 1912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211949
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.972662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1045246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.55422.92782
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.85715282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.4591515
X-RAY DIFFRACTIONr_chiral_restr0.1020.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021497
X-RAY DIFFRACTIONr_nbd_refined0.2510.21010
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21332
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.296
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3260.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3330.24
X-RAY DIFFRACTIONr_mcbond_it0.6781.51261
X-RAY DIFFRACTIONr_mcangle_it1.17621950
X-RAY DIFFRACTIONr_scbond_it1.5153812
X-RAY DIFFRACTIONr_scangle_it2.4764.5712
LS refinement shellResolution: 2.95→3.027 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 29 -
Rwork0.306 595 -
obs-624 100 %
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)
14.83210.75061.68193.4987-0.57714.25740.08590.4342-0.0128-0.1112-0.1637-0.38990.27930.44930.0778-0.05340.0635-0.103-0.12120.1012-0.061717.161562.435743.8368
25.7752-1.07361.43447.32550.40065.312-0.0252-0.99791.30050.5213-0.5648-0.0652-0.7479-0.21670.590.1575-0.031-0.21810.0969-0.1940.163614.449576.66661.2065
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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