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- PDB-9kf1: Crystal structure of Streptomyces sp. sulfotransferase Cpz8 invol... -

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Basic information

Entry
Database: PDB / ID: 9kf1
TitleCrystal structure of Streptomyces sp. sulfotransferase Cpz8 involved in Caprazamycins Synthesis
ComponentsSulfotransferase family protein
KeywordsBIOSYNTHETIC PROTEIN / sulfotransferase
Function / homologySulfotransferase, S. mansonii-type / Sulfotransferase domain / transferase activity / P-loop containing nucleoside triphosphate hydrolase / PHOSPHATE ION / Sulfotransferase family protein
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsIwamoto, Y. / Watanabe, M. / Suzuki, K. / Teramoto, T. / Kakuta, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24K09353 Japan
CitationJournal: To Be Published
Title: Crystal structure of Streptomyces sp. sulfotransferase Cpz8 involved in Caprazamycin Synthesis
Authors: Iwamoto, Y. / Watanabe, M. / Kawano, K. / Suzuki, K. / Yazaki, M. / Arisawa, M. / Nishimoto, E. / Igarashi, M. / Teramoto, T. / Kakuta, Y.
History
DepositionNov 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sulfotransferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4474
Polymers24,2321
Non-polymers2143
Water6,233346
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.420, 33.040, 64.240
Angle α, β, γ (deg.)90.000, 102.881, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

#1: Protein Sulfotransferase family protein


Mass: 24232.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Gene: G3M58_47930 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6G3X8Q2
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: Sodium phosphate monohydrate monobasic, potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→50 Å / Num. obs: 54909 / % possible obs: 99.8 % / Redundancy: 7.8 % / CC1/2: 0.99 / Net I/σ(I): 18.1
Reflection shellResolution: 1.38→1.41 Å / Num. unique obs: 3690 / CC1/2: 0.89

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TIZ

5tiz


Resolution: 1.38→31.54 Å / SU ML: 0.1455 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.112
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1537 2000 3.64 %
Rwork0.1416 52903 -
obs0.1421 54903 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.68 Å2
Refinement stepCycle: LAST / Resolution: 1.38→31.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 11 346 1997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01131856
X-RAY DIFFRACTIONf_angle_d1.19632552
X-RAY DIFFRACTIONf_chiral_restr0.0924264
X-RAY DIFFRACTIONf_plane_restr0.0159339
X-RAY DIFFRACTIONf_dihedral_angle_d14.1812689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.410.34911390.32453688X-RAY DIFFRACTION98.76
1.41-1.450.27351420.25833740X-RAY DIFFRACTION99.44
1.45-1.50.23091420.20323759X-RAY DIFFRACTION99.92
1.5-1.540.22271410.17753716X-RAY DIFFRACTION99.9
1.54-1.60.18971420.16363772X-RAY DIFFRACTION99.9
1.6-1.660.17351420.15183759X-RAY DIFFRACTION99.97
1.66-1.740.16331430.15473782X-RAY DIFFRACTION99.9
1.74-1.830.17761420.15293739X-RAY DIFFRACTION99.95
1.83-1.950.15431440.13673799X-RAY DIFFRACTION99.97
1.95-2.10.14121410.12993773X-RAY DIFFRACTION100
2.1-2.310.13811440.12353793X-RAY DIFFRACTION99.97
2.31-2.640.14431430.12243796X-RAY DIFFRACTION99.97
2.64-3.320.14491460.12713845X-RAY DIFFRACTION100
3.33-31.540.12751490.13393942X-RAY DIFFRACTION99.83
Refinement TLS params.Method: refined / Origin x: 18.7934035275 Å / Origin y: 7.29365796698 Å / Origin z: 10.9264925468 Å
111213212223313233
T0.130977407242 Å20.0132687815394 Å20.00981206924088 Å2-0.101351524528 Å2-0.00917308164122 Å2--0.13650707401 Å2
L0.558215470401 °2-0.0694443896627 °2-0.139675995007 °2-1.58037675372 °20.0468967775026 °2--1.75478265242 °2
S0.00408173307008 Å °0.0275277727948 Å °-0.0154409408362 Å °-0.0939477410778 Å °-0.042655457306 Å °0.178718376372 Å °-0.0452940056368 Å °-0.146465030811 Å °0.0263113002156 Å °
Refinement TLS groupSelection details: all

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