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- PDB-7qzj: 1.55 A X-ray crystallographic structure of SapH from Streptomyces... -

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Basic information

Entry
Database: PDB / ID: 7qzj
Title1.55 A X-ray crystallographic structure of SapH from Streptomyces sp. (HPH0547) involved in Pseudouridimycin biosynthesis
ComponentsAspartate aminotransferase family protein
KeywordsBIOSYNTHETIC PROTEIN / Pseudouridimycin / Streptomyces / antibiotics / Pyridoxal phosphate / secondary metabolism
Function / homology
Function and homology information


adenosylmethionine-8-amino-7-oxononanoate transaminase activity / biotin biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
: / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Adenosylmethionine-8-amino-7-oxononanoate transaminase
Similarity search - Component
Biological speciesStreptomyces sp. HPH0547 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSchnell, R. / Schneider, G.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2018-03999 Sweden
CitationJournal: Acs Chem.Biol. / Year: 2023
Title: Pseudouridine-Modifying Enzymes SapB and SapH Control Entry into the Pseudouridimycin Biosynthetic Pathway.
Authors: Artukka, E. / Schnell, R. / Palmu, K. / Rosenqvist, P. / Szodorai, E. / Niemi, J. / Virta, P. / Schneider, G. / Metsa-Ketela, M.
History
DepositionJan 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aspartate aminotransferase family protein
B: Aspartate aminotransferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2569
Polymers95,4582
Non-polymers7987
Water16,105894
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, Analytical size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.581, 63.191, 211.415
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aspartate aminotransferase family protein / SapH


Mass: 47729.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal Hexahistidine tag used for purification is present on the crystallized protein. Sequence: MAHHHHHHHRS.
Source: (gene. exp.) Streptomyces sp. HPH0547 (bacteria) / Gene: HMPREF1486_04341 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: S3AT34
#2: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N2O5P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 894 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.2 Å3/Da / Density % sol: 43.9 % / Description: diamond shape
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M BTP pH 7.5 0.2M Na-K-Phosphate 27.5% PEG3350

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2020 / Details: KB mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.55→44.47 Å / Num. obs: 121033 / % possible obs: 98.8 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 6.4 % / Biso Wilson estimate: 15.8 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.046 / Net I/σ(I): 11.1
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5292 / CC1/2: 0.679 / Rpim(I) all: 0.509 / % possible all: 88.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GHG

5ghg


Resolution: 1.55→44.47 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.498 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1823 5991 5 %RANDOM
Rwork0.1595 ---
obs0.1606 114927 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.22 Å2 / Biso mean: 23.519 Å2 / Biso min: 10.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.85 Å2-0 Å2
3----1 Å2
Refinement stepCycle: final / Resolution: 1.55→44.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6275 0 47 894 7216
Biso mean--28.9 35.86 -
Num. residues----844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196501
X-RAY DIFFRACTIONr_bond_other_d0.0020.026319
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.988868
X-RAY DIFFRACTIONr_angle_other_deg0.957314437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7175854
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.91521.734271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08215973
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0691576
X-RAY DIFFRACTIONr_chiral_restr0.0830.21024
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217457
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021485
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 391 -
Rwork0.268 7592 -
all-7983 -
obs--89.22 %

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