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- PDB-7vmw: Crystal structure of LimF prenyltransferase bound with a peptide ... -

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Basic information

Entry
Database: PDB / ID: 7vmw
TitleCrystal structure of LimF prenyltransferase bound with a peptide substrate and GSPP
Components
  • LynF/TruF/PatF family peptide O-prenyltransferase
  • substrate peptide
KeywordsTRANSFERASE / ripp / prenylation / prenyltransferase / abba fold
Function / homologyPeptide O-prenyltransferase, LynF/TruF/PatF family / Family of unknown function (DUF5838) / transferase activity / GERANYL S-THIOLODIPHOSPHATE / PYROPHOSPHATE / LynF/TruF/PatF family peptide O-prenyltransferase
Function and homology information
Biological speciesLimnothrix sp. CACIAM 69d (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsHamada, K. / Kobayashi, S. / Okada, C. / Zhang, Y. / Inoue, S. / Goto, Y. / Suga, H. / Ogata, K. / Sengoku, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Catal / Year: 2022
Title: LimF is a versatile prenyltransferase for histidine-C-geranylation on diverse non-natural substrates
Authors: Zhang, Y. / Hamada, K. / Nguyen, D.T. / Inoue, S. / Satake, M. / Kobayashi, S. / Okada, C. / Ogata, K. / Okada, M. / Sengoku, T. / Goto, Y. / Suga, H.
History
DepositionOct 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Aug 24, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LynF/TruF/PatF family peptide O-prenyltransferase
B: LynF/TruF/PatF family peptide O-prenyltransferase
C: substrate peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5317
Polymers69,9743
Non-polymers5574
Water7,620423
1
A: LynF/TruF/PatF family peptide O-prenyltransferase
C: substrate peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6034
Polymers35,2482
Non-polymers3552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-12 kcal/mol
Surface area14570 Å2
MethodPISA
2
B: LynF/TruF/PatF family peptide O-prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9283
Polymers34,7261
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-12 kcal/mol
Surface area14930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.660, 48.430, 91.040
Angle α, β, γ (deg.)90.000, 117.869, 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

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Protein / Protein/peptide , 2 types, 3 molecules ABC

#1: Protein LynF/TruF/PatF family peptide O-prenyltransferase


Mass: 34725.676 Da / Num. of mol.: 2
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: Protein/peptide substrate peptide


Mass: 522.599 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 427 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GST / GERANYL S-THIOLODIPHOSPHATE / S-[(2E)-3,7-DIMETHYLOCTA-2,6-DIENYL] TRIHYDROGEN THIODIPHOSPHATE


Mass: 330.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O6P2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PPV / PYROPHOSPHATE / Pyrophosphate


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: PEG 1500, PCB (Na propionate, Na cacodylate, bis-tris propane) buffer, magnesium chloride

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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: Jul 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→40.24 Å / Num. obs: 52412 / % possible obs: 99.96 % / Redundancy: 6.9 % / Biso Wilson estimate: 33.08 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.67
Reflection shellResolution: 1.93→2 Å / Num. unique obs: 5193 / CC1/2: 0.508

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TTY

5tty


Resolution: 1.93→40.24 Å / SU ML: 0.2853 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.2409
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2316 2006 3.83 %
Rwork0.1824 50405 -
obs0.1843 52411 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.92 Å2
Refinement stepCycle: LAST / Resolution: 1.93→40.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4812 0 34 423 5269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01345002
X-RAY DIFFRACTIONf_angle_d1.2286784
X-RAY DIFFRACTIONf_chiral_restr0.0737736
X-RAY DIFFRACTIONf_plane_restr0.0108880
X-RAY DIFFRACTIONf_dihedral_angle_d11.5829672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.41111480.37563564X-RAY DIFFRACTION99.95
1.98-2.030.37751480.29373571X-RAY DIFFRACTION100
2.03-2.090.27731400.22863566X-RAY DIFFRACTION100
2.09-2.160.25441370.20833555X-RAY DIFFRACTION100
2.16-2.240.25511380.20753615X-RAY DIFFRACTION99.97
2.24-2.330.26431480.21083558X-RAY DIFFRACTION99.95
2.33-2.430.27741510.20823579X-RAY DIFFRACTION100
2.43-2.560.2691460.1933586X-RAY DIFFRACTION99.97
2.56-2.720.2241400.18963584X-RAY DIFFRACTION100
2.72-2.930.27591390.19353595X-RAY DIFFRACTION100
2.93-3.220.24881380.17833640X-RAY DIFFRACTION100
3.22-3.690.18231390.15843613X-RAY DIFFRACTION99.97
3.69-4.650.17661410.14373643X-RAY DIFFRACTION100
4.65-40.240.21831530.16863736X-RAY DIFFRACTION99.82
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)
12.186012985240.835261477995-1.19600248212.61833729561-0.7062505985614.039912520710.0515459991437-0.0310261762752-0.04965145066230.0413824454156-0.01792195771180.264976653458-0.0248808931498-0.120514863606-0.02647668591750.1423881212210.00644726584966-0.007780633683570.131339529548-0.008840167929520.198013940921-5.9139268829113.7383107734-32.370546219
22.94194576612-0.3428981825520.1326473699592.22299875083-0.0843018970563.98247238413-0.0231874612355-0.189187218235-0.2211764017770.0380623625730.0521991386334-0.03890145272320.1238766065730.235738217111-0.03308950882310.2166785379320.004661365255290.02618205834960.183501859192-0.001145795906680.2494130209385.02619832261-1.15335806443-28.5601676248
32.22317479797-0.592759666225-0.1392178815642.293485245380.04437467206691.07320792888-0.0915942278425-0.2915311333180.2946379357120.2139941051670.137438835701-0.295796126066-0.1020722288650.200633136817-0.03915858631370.205525379194-0.0111479351945-0.008647809486590.238073957453-0.05758415518050.20595110950913.822383800918.6271164408-27.8234459902
41.89655952903-0.7952992125040.521932034022.67457728767-0.4229654450131.738113552140.1035221221170.184210010079-0.01337237485040.0504256272656-0.1147321752190.0540240108176-0.06685279872250.1013433372930.02499904093090.19093545565-0.01257297805420.0155139523830.199307518398-0.03350479086240.158777955409-22.124908645316.0119702206-62.6135563765
50.1538407122450.4845185307540.241806641413.976500168021.34774389586.539074456840.03002077008260.258222914211-0.121953035188-0.920717992520.00968663484240.002765612201480.405230406748-0.677934529014-0.04062077366540.494538507788-0.050211581842-0.009973459794830.594973964583-0.02821653254680.29726247829-17.096911573210.3462268701-80.9987722897
66.021583637920.27296438215-1.228379548464.578554569110.2155415211534.63622349358-0.1448356285410.874284487289-0.197637494987-0.6116937207780.0741611066548-0.2490751078880.1963197971340.2426401892410.09326707302370.333217197028-0.00139440069060.00523248720580.348349980738-0.05424687660110.277857115902-14.2937356115-0.440587853835-70.633879472
73.70405150189-3.9383288924.110027014284.20115478555-4.342669544514.618436219780.194865348368-1.267761218060.3920239642341.303576473371.163687943440.8062659906020.201932129227-0.842170127644-1.348569020280.5332004316980.07661805338410.01145368157420.7891819662960.03449680461080.4827341721465.8235551311212.3807680652-20.9721584329
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 77 )AA7 - 771 - 71
22chain 'A' and (resid 78 through 182 )AA78 - 18272 - 176
33chain 'A' and (resid 183 through 302 )AA183 - 302177 - 296
44chain 'B' and (resid 7 through 165 )BD7 - 1651 - 159
55chain 'B' and (resid 166 through 225 )BD166 - 225160 - 219
66chain 'B' and (resid 226 through 300 )BD226 - 300220 - 294
77chain 'C' and (resid 1 through 5 )CH1 - 52 - 6

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