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- PDB-7vmy: Crystal structure of LimF prenyltransferase bound with GSPP -

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Basic information

Entry
Database: PDB / ID: 7vmy
TitleCrystal structure of LimF prenyltransferase bound with GSPP
ComponentsLynF/TruF/PatF family peptide O-prenyltransferase
KeywordsTRANSFERASE / ripp / prenylation / prenyltransferase / abba fold
Function / homologyPeptide O-prenyltransferase, LynF/TruF/PatF family / Family of unknown function (DUF5838) / transferase activity / GERANYL S-THIOLODIPHOSPHATE / LynF/TruF/PatF family peptide O-prenyltransferase
Function and homology information
Biological speciesLimnothrix sp. CACIAM 69d (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,5798
Polymers69,4512
Non-polymers1,1286
Water6,485360
1
A: LynF/TruF/PatF family peptide O-prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2894
Polymers34,7261
Non-polymers5643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-12 kcal/mol
Surface area13990 Å2
MethodPISA
2
B: LynF/TruF/PatF family peptide O-prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2894
Polymers34,7261
Non-polymers5643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-11 kcal/mol
Surface area14240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.280, 47.520, 61.190
Angle α, β, γ (deg.)100.124, 104.693, 96.679
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#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: 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-GST / GERANYL S-THIOLODIPHOSPHATE / S-[(2E)-3,7-DIMETHYLOCTA-2,6-DIENYL] TRIHYDROGEN THIODIPHOSPHATE


Mass: 330.275 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H20O6P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 1.86 Å3/Da / Density % sol: 33.79 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: Mg(OAc)2, PEG 3350, bis-tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.77→31.52 Å / Num. obs: 47519 / % possible obs: 97.38 % / Redundancy: 6.1 % / Biso Wilson estimate: 24.76 Å2 / CC1/2: 0.996 / Net I/σ(I): 12.52
Reflection shellResolution: 1.77→1.83 Å / Num. unique obs: 4671 / CC1/2: 0.765

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Processing

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

5tty


Resolution: 1.77→31.52 Å / SU ML: 0.2303 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 22.9824
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2098 2005 4.22 %
Rwork0.17 45464 -
obs0.1717 47469 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.11 Å2
Refinement stepCycle: LAST / Resolution: 1.77→31.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4773 0 68 360 5201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01274985
X-RAY DIFFRACTIONf_angle_d1.41926757
X-RAY DIFFRACTIONf_chiral_restr0.0817727
X-RAY DIFFRACTIONf_plane_restr0.0112875
X-RAY DIFFRACTIONf_dihedral_angle_d18.9785682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.810.35621380.26213244X-RAY DIFFRACTION95.86
1.81-1.860.27881390.23023186X-RAY DIFFRACTION96.21
1.86-1.920.23821430.19843203X-RAY DIFFRACTION96.32
1.92-1.980.22791380.18463246X-RAY DIFFRACTION96.55
1.98-2.050.24071510.18193209X-RAY DIFFRACTION97.05
2.05-2.130.25371360.18693229X-RAY DIFFRACTION96.83
2.13-2.230.24581400.18983238X-RAY DIFFRACTION97.35
2.23-2.350.2651470.17333267X-RAY DIFFRACTION97.54
2.35-2.490.21121440.18153244X-RAY DIFFRACTION97.72
2.49-2.690.23871490.18223246X-RAY DIFFRACTION97.64
2.69-2.960.23761490.18453290X-RAY DIFFRACTION98.12
2.96-3.380.19681410.16293283X-RAY DIFFRACTION98.31
3.38-4.260.16391470.13993274X-RAY DIFFRACTION98.96
4.26-31.520.1721430.15533305X-RAY DIFFRACTION99.08
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)
12.92221458839-0.43552031941-0.7511002394112.028961185930.5287408788433.142794647070.1283971228380.2528968554220.129227575379-0.2621964271560.04942238535860.1598469170590.012269474605-0.2635498759880.02769908204590.175578268565-0.00754336900097-0.02652937483010.1550208099790.02794220407830.19577957609730.014953859368.865711891240.4942862325
23.04220538885-0.3294776437350.03835475057182.515713276570.0762597978642.07436880.0265512257679-0.2257400965120.1041560593020.154729484382-0.0789689897072-0.0380626969074-0.0670722808052-0.14076577201-0.006662270787330.1198210351-0.003406113645090.007336387838910.1693756173880.007367559442960.12459120693329.897955446265.055517850751.5337134052
32.602799576410.4330319940240.01296870137743.366954998140.5056321841382.91506954194-0.0457873124201-0.0505985707445-0.3305638849970.0248576970239-0.01781595275060.1592016933810.214549546054-0.1003050117820.02568021135930.1106195010550.01615222548650.02367621259450.189587893818-0.007626267691420.20199677307832.308748106349.69403627955.6809118941
43.06513701917-0.7450762363040.3800086681981.20554559908-0.369909880770.8660645601280.0170915367246-0.145510405319-0.5956410348860.06870051656920.08839534759660.3440957902110.0201801291093-0.178095421007-0.1076355130580.18049525846-0.01541921565840.04527216594230.2468612531360.003918550972760.29394501388214.809790502451.516112886958.3188265177
54.42428589581-0.03401569570360.2895623062841.6347734168-0.6329299637231.089252031760.123234248332-0.1599231807010.474128180071-0.0140235850519-0.02500662494040.193867014285-0.1427341599270.05636202098870.02770458186020.20603338683-0.01105874879950.02396446841310.255561590273-0.01982925665860.20731360293611.215569445671.591983029654.7499392923
64.067094455480.031344445807-0.1357379421164.47359389748-0.1219456209883.40294648850.0284830501296-0.217948607780.3119027953510.1427532882580.2157216119510.3391526229810.112394111812-0.363937036829-0.1112787896410.1005292090060.0199916391766-0.006935712029270.239418015384-0.009253678787340.17963254242716.404348490463.241647420752.2971309799
71.92096331472-0.1563242375320.1057805498132.1057854490.478840595581.274504808340.00194558661863-0.0997136771059-0.003025997645910.0471956642542-0.0142917321940.0230835291922-0.0192430654111-0.03017916247560.007198494865740.149913954465-0.008675725382050.007074261919160.1089011288190.01592976455570.1195207169760.99545832119428.689310333735.4590703938
83.444065807871.010700850.3438214742743.852231422270.2330837632852.780444703460.04210681302430.1016076546620.243133877235-0.0659082871814-0.0245125590311-0.40151996454-0.1268908371290.200560052635-0.03262548001610.1729460234990.00957550085910.002772427577170.1188414993590.01440688042050.18809863244115.664638655332.044691640725.7280932855
91.27988151481-0.498704049507-0.5036247921412.631504241960.04818858201390.5908953812080.0383722640701-0.01353942015570.17721303935-0.02214158914030.0263575306714-0.0981561267502-0.116492199739-0.00302909153305-0.05099270160010.184485182448-0.0016072246007-0.004047482823380.1377475162090.001336784049180.1230135070024.0338108025546.585657666527.0796500188
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 9 through 30 )AA9 - 301 - 22
22chain 'A' and (resid 31 through 77 )AA31 - 7723 - 69
33chain 'A' and (resid 78 through 169 )AA78 - 16970 - 161
44chain 'A' and (resid 170 through 242 )AA170 - 242162 - 234
55chain 'A' and (resid 243 through 265 )AA243 - 265235 - 257
66chain 'A' and (resid 266 through 302 )AA266 - 302258 - 294
77chain 'B' and (resid 8 through 94 )BE8 - 941 - 87
88chain 'B' and (resid 95 through 170 )BE95 - 17088 - 163
99chain 'B' and (resid 171 through 302 )BE171 - 302164 - 295

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