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- PDB-5jxm: Crystal Structure of Prenyltransferase PriB Apo Form -

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Basic information

Entry
Database: PDB / ID: 5jxm
TitleCrystal Structure of Prenyltransferase PriB Apo Form
ComponentsPriB
KeywordsTRANSFERASE / Prenyltransferase / 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 / Prenyltransferase
Function and homology information
Biological speciesStreptomyces sp. RM-5-8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.15 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, 4items
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)R01CA203257 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37AI52188 United States
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)UL1TR000117 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
DepositionMay 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 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 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PriB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5473
Polymers43,4011
Non-polymers1462
Water10,989610
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.526, 83.723, 41.527
Angle α, β, γ (deg.)90.000, 106.270, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-731-

HOH

21A-911-

HOH

31A-1098-

HOH

41A-1195-

HOH

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Components

#1: Protein PriB


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) / Strain: rm-5-8 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A182DWE5*PLUS
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 610 / 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: 1.99 Å3/Da / Density % sol: 38.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
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 L-Tryptophan and 1 mM daptomycin with reservoir solution ...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 L-Tryptophan and 1 mM daptomycin with reservoir solution containing 0.1 M Tris pH 8.5, 20% w/v PEG 3350, 0.1 M MgCl2. The mixed drops of 0.4-1 uL were equilibrated over a reservoir solution of 50 uL and incubated at 20oC in the dark. The iodine derivative was prepared by 1:3 v/v soaking a solution of 0.5 M sodium iodide, 0.05 M Tris pH 8.5, 10% w/v PEG 3350, 0.05 M MgCl2 into PriB crystals

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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: 1.08→49.691 Å / Num. obs: 131276 / % possible obs: 90.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 13.88 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Net I/σ(I): 8.15
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.08-1.152.6020.32151.9
1.15-1.231.5130.75190.3
1.23-1.320.8731.51199.7
1.32-1.450.4572.86199.8
1.45-1.620.215.99199.8
1.62-1.870.10111.55199.8
1.87-2.290.05819.54199.7
2.29-3.240.04327.24199.7
3.24-49.6910.03832.1198.6

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Phasing

PhasingMethod: molecular replacement

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Processing

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

5inj


Resolution: 1.15→27.555 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.42
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 3647 1.69 %Random selection
Rwork0.1786 216176 --
obs0.1792 117867 90.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.72 Å2 / Biso mean: 23.4948 Å2 / Biso min: 5.7 Å2
Refinement stepCycle: final / Resolution: 1.15→27.555 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2691 0 21 610 3322
Biso mean--19.26 34.38 -
Num. residues----356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0183015
X-RAY DIFFRACTIONf_angle_d1.5164148
X-RAY DIFFRACTIONf_chiral_restr0.099456
X-RAY DIFFRACTIONf_plane_restr0.011572
X-RAY DIFFRACTIONf_dihedral_angle_d18.6681134
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.15-1.16510.4172860.43265193527958
1.1651-1.18110.42811130.43786409652271
1.1811-1.1980.44661240.40457400752483
1.198-1.21590.40621330.38617867800088
1.2159-1.23490.33941390.34628115825490
1.2349-1.25510.38581380.34588153829190
1.2551-1.27670.31561420.32678068821090
1.2767-1.30.35051420.30888273841591
1.3-1.3250.29161360.29858046818291
1.325-1.3520.33281450.28528269841491
1.352-1.38140.28071430.26928314845792
1.3814-1.41350.28661420.26378193833592
1.4135-1.44890.28111520.26198358851093
1.4489-1.48810.27181450.24028330847593
1.4881-1.53180.21111440.20768432857693
1.5318-1.58130.21791430.19828381852494
1.5813-1.63780.21131400.18668472861294
1.6378-1.70330.19541450.17448495864095
1.7033-1.78090.20391470.17588543869095
1.7809-1.87470.19021480.16958599874795
1.8747-1.99220.19751450.16198657880296
1.9922-2.14590.16711480.15348702885097
2.1459-2.36180.19981530.14728706885997
2.3618-2.70330.20231510.14738839899098
2.7033-3.40480.16091560.13838880903699
3.4048-27.5630.18521470.1368835898298

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