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- PDB-5k9m: Crystal Structure of PriB Binary Complex with Product Diphosphate -

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Basic information

Entry
Database: PDB / ID: 5k9m
TitleCrystal Structure of PriB Binary Complex with Product Diphosphate
ComponentsPriB Prenyltransferase
KeywordsTRANSFERASE / Prenyltransferase / diphosphate / indole-PT / ABBA family / PT fold / Structural Genomics / PSI-2 / Protein Structure Initiative / Enzyme Discovery for Natural Product Biosynthesis / NatPro
Function / homologyAromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase / alkaloid metabolic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / PYROPHOSPHATE 2- / Prenyltransferase
Function and homology information
Biological speciesStreptomyces sp. RM-5-8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsCao, H. / Elshahawi, S. / Benach, J. / Wasserman, S.R. / Morisco, L.L. / Koss, J.W. / Thorson, J.S. / Phillips Jr., G.N. / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U01GM098248 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA84374 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37AI52188 United States
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Structure and specificity of a permissive bacterial C-prenyltransferase.
Authors: Elshahawi, S.I. / Cao, H. / Shaaban, K.A. / Ponomareva, L.V. / Subramanian, T. / Farman, M.L. / Spielmann, H.P. / Phillips, G.N. / Thorson, J.S. / Singh, S.
History
DepositionJun 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Feb 22, 2017Group: Database references
Revision 1.3Mar 29, 2017Group: Database references
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 23, 2020Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.7Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PriB Prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6993
Polymers43,4011
Non-polymers2982
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.727, 83.020, 95.304
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-934-

HOH

21A-1024-

HOH

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Components

#1: Protein PriB Prenyltransferase


Mass: 43400.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. RM-5-8 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A182DWE5*PLUS
#2: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 1.9 Å3/Da / Density % sol: 35.32 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PriB was crystallized by sitting drop vapor diffusion method by 1:1 v/v mixing of 10 mg/mL PriB solution in the presence of 1 mM daptomycin and 1 mM Dimethylallyl diphosphate (DMAPP) with ...Details: PriB was crystallized by sitting drop vapor diffusion method by 1:1 v/v mixing of 10 mg/mL PriB solution in the presence of 1 mM daptomycin and 1 mM Dimethylallyl diphosphate (DMAPP) with reservoir solution containing 0.1 M Tris pH 8, 28% w/v PEG 4000. The mixed drops of 0.4 uL were equilibrated over a reservoir solution of 50 uL and incubated at 20oC in the dark.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.5→38.224 Å / Num. obs: 101546 / % possible obs: 99.71 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.59
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 1.7 % / Rmerge(I) obs: 1.9 / Mean I/σ(I) obs: 1.7 / % possible all: 99.79

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5INJ

5inj


Resolution: 1.5→38.224 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.61
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3052 3.01 %Random Selection
Rwork0.1935 ---
obs0.1945 101416 98.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.26 Å2 / Biso mean: 27.3616 Å2 / Biso min: 10.27 Å2
Refinement stepCycle: final / Resolution: 1.5→38.224 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2663 0 29 426 3118
Biso mean--37.6 35.28 -
Num. residues----353
LS refinement shellResolution: 1.5→1.5234 Å
RfactorNum. reflection% reflection
Rfree0.3929 131 -
Rwork0.4106 4234 -
obs-4365 94 %

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