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- PDB-8je4: Crystal structure of LimF prenyltransferase (H239G/W273T mutant) ... -

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Basic information

Entry
Database: PDB / ID: 8je4
TitleCrystal structure of LimF prenyltransferase (H239G/W273T mutant) bound with the thiodiphosphate moiety of farnesyl S-thiolodiphosphate (FSPP)
Componentsprenyltransferase, LimF
KeywordsTRANSFERASE / ripp / prenylation / abba fold
Function / homologyPeptide O-prenyltransferase, LynF/TruF/PatF family / Family of unknown function (DUF5838) / transferase activity / metal ion binding / TRIHYDROGEN THIODIPHOSPHATE / LynF/TruF/PatF family peptide O-prenyltransferase
Function and homology information
Biological speciesLimnothrix sp. CACIAM 69d (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsHamada, K. / Oguni, A. / Zhang, Y. / Satake, M. / Goto, Y. / Suga, H. / Ogata, K. / Sengoku, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Switching Prenyl Donor Specificities of Cyanobactin Prenyltransferases.
Authors: Zhang, Y. / Hamada, K. / Satake, M. / Sengoku, T. / Goto, Y. / Suga, H.
History
DepositionMay 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: prenyltransferase, LimF
B: prenyltransferase, LimF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5546
Polymers69,1192
Non-polymers4354
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-12 kcal/mol
Surface area14520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.980, 47.880, 89.460
Angle α, β, γ (deg.)90.000, 117.656, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein prenyltransferase, LimF


Mass: 34559.473 Da / Num. of mol.: 2 / Mutation: H239G, W273T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Limnothrix sp. CACIAM 69d (bacteria) / Gene: BJG00_018450 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A372DCN7
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PIS / TRIHYDROGEN THIODIPHOSPHATE / THIOPYROPHOSPHATE


Mass: 193.033 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H3O6P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 6.5, 25% Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→44.69 Å / Num. obs: 34791 / % possible obs: 99.95 % / Redundancy: 2 % / Biso Wilson estimate: 30.94 Å2 / CC1/2: 0.993 / Net I/σ(I): 6.67
Reflection shellResolution: 2.19→2.268 Å / Num. unique obs: 3428 / CC1/2: 0.594

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→44.69 Å / SU ML: 0.2866 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9069
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2483 3416 9.82 %
Rwork0.2066 31366 -
obs0.2107 34782 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.35 Å2
Refinement stepCycle: LAST / Resolution: 2.19→44.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4678 0 20 203 4901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00234804
X-RAY DIFFRACTIONf_angle_d0.51486505
X-RAY DIFFRACTIONf_chiral_restr0.0451717
X-RAY DIFFRACTIONf_plane_restr0.0053841
X-RAY DIFFRACTIONf_dihedral_angle_d12.36211773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.220.30021310.30741284X-RAY DIFFRACTION99.93
2.22-2.250.36131390.29661325X-RAY DIFFRACTION99.93
2.25-2.290.34021660.29581270X-RAY DIFFRACTION99.93
2.29-2.330.30581240.28031253X-RAY DIFFRACTION99.93
2.33-2.370.32461410.26991334X-RAY DIFFRACTION100
2.37-2.410.31651540.26971299X-RAY DIFFRACTION99.93
2.41-2.460.26561270.26141271X-RAY DIFFRACTION100
2.46-2.510.25831510.2461297X-RAY DIFFRACTION100
2.51-2.560.30011340.24291309X-RAY DIFFRACTION99.86
2.56-2.620.24711470.2281289X-RAY DIFFRACTION100
2.62-2.690.29291410.22381302X-RAY DIFFRACTION100
2.69-2.760.28691470.23341277X-RAY DIFFRACTION100
2.76-2.840.27751520.22831303X-RAY DIFFRACTION100
2.84-2.930.28811380.22581294X-RAY DIFFRACTION100
2.93-3.040.25911440.2171312X-RAY DIFFRACTION100
3.04-3.160.24981350.21131326X-RAY DIFFRACTION100
3.16-3.30.27981450.19391301X-RAY DIFFRACTION100
3.3-3.480.24691440.18191308X-RAY DIFFRACTION100
3.48-3.690.22881420.18811321X-RAY DIFFRACTION100
3.69-3.980.21641440.17771302X-RAY DIFFRACTION100
3.98-4.380.18461450.16651331X-RAY DIFFRACTION100
4.38-5.010.20971350.1561324X-RAY DIFFRACTION100
5.01-6.310.20471420.19711350X-RAY DIFFRACTION100
6.31-44.690.22521480.18491384X-RAY DIFFRACTION99.8
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)
11.824159846510.2659834975470.1034884626172.682570878250.3730853987491.24427173096-0.0001012323334420.1259250508910.147200829463-0.239118036681-0.00586031933502-0.0642139518333-0.1060118064740.028807034510.01227597981440.2781027103670.02383822167350.009782251433150.1461672149750.03415706397870.19737543947542.6945063724-6.4495467849222.29462135
21.41307218365-0.1839862314760.49933532723.94724565513-2.2646777174.382548638690.00554347630055-0.353189670266-0.08630768866410.7826420538350.08952328345820.037272547127-0.1577929381980.0736357494612-0.1375131995890.3915996133130.04682000176820.02232792035720.2502126369360.01122157545320.24944616182140.0216800451-4.6707360208743.3826575176
33.6443896159-2.611564314530.05552693795936.897691781721.119817685343.940911400220.109041648165-0.17349436904-0.18110736317-0.1634509241490.07047382603330.3564687338850.277913093318-0.222209465436-0.1920127595150.275101146828-0.02995217380230.01185696191120.1819388547960.03068180265610.21627859446335.8664062684-14.898719224942.7661809469
42.43121345397-0.356550741009-1.423473870553.103950788970.4440445657413.29527620023-0.131890365541-0.151169233961-0.1665415541120.168696025310.00826679430859-0.01418467957690.3204685221210.0676266341010.162869214720.300874158056-0.01470886397560.007741110666490.1575739888050.0479467751990.28754962238437.3096598548-23.308652388532.2030939822
51.401866252450.1327578370280.6571846714292.554261221380.6933755830363.14358168387-0.0063431221594-0.0392339237139-0.0971412547605-0.0533471419111-0.0441260892899-0.10238383079-0.0152224801598-0.1587687621180.05868451778720.2378769955660.01851709107630.03214739991680.1996449570940.02720926845210.19622295854723.2290097334-16.0902090133-9.10927050776
62.958821353720.7519004890810.4791597585622.6185760454-0.4588008639740.7904983075720.00362918605-0.01384560078030.3841863212680.01887095573910.09047297290690.34921439364-0.243915242973-0.565329727322-0.1128108353390.3983849000780.1109738651940.01904153370710.4623233168620.04809959067110.27788685720210.3370696124-1.03226608542-9.50664775295
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 7 through 145 )AA7 - 1451 - 139
22chain 'A' and (resid 146 through 210 )AA146 - 210140 - 204
33chain 'A' and (resid 211 through 240 )AA211 - 240205 - 234
44chain 'A' and (resid 241 through 301 )AA241 - 301235 - 295
55chain 'B' and (resid 7 through 182 )BD7 - 1821 - 176
66chain 'B' and (resid 183 through 300 )BD183 - 300177 - 289

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