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- PDB-9vt8: Crystal structure of SmiF bound with a substrate peptide and DMASPP -

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Basic information

Entry
Database: PDB / ID: 9vt8
TitleCrystal structure of SmiF bound with a substrate peptide and DMASPP
Components
  • HIS-PRO-TRP-GLY-VAL
  • SmiF
KeywordsTRANSFERASE / prenyltransferase
Function / homologyDIMETHYLALLYL S-THIOLODIPHOSPHATE
Function and homology information
Biological speciesScytonema millei (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsInoue, S. / Hamada, K. / Goto, Y. / Suga, H. / Sengoku, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Nat Catal
Title: Rapid screening platform for peptide prenyltransferases to diversify pseudo-natural prenylated peptides
Authors: Inoue, S.
History
DepositionJul 10, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SmiF
B: HIS-PRO-TRP-GLY-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0263
Polymers34,7642
Non-polymers2621
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-13 kcal/mol
Surface area12710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.200, 61.950, 118.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein SmiF


Mass: 34144.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Uniparc:UPI000847B08D / Source: (gene. exp.) Scytonema millei (bacteria) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide HIS-PRO-TRP-GLY-VAL


Mass: 619.715 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O6P2S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: 2.66 Å3/Da / Density % sol: 53.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.3 M KSCN, 100 mM Tris pH 8-9, 1.04-1.10 M NaK-tartrate tetrahydrate

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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: Jun 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→42.9 Å / Num. all: 692776 / Num. obs: 10153 / % possible obs: 99.93 % / Redundancy: 68.3 % / Biso Wilson estimate: 64.64 Å2 / CC1/2: 0.992 / Net I/σ(I): 21.54
Reflection shellResolution: 2.75→2.848 Å / Num. unique obs: 987 / CC1/2: 0.798

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.75→42.9 Å / SU ML: 0.4225 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.7067
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2635 1016 10.01 %
Rwork0.2046 9132 -
obs0.2107 10148 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.04 Å2
Refinement stepCycle: LAST / Resolution: 2.75→42.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2300 0 14 0 2314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01282368
X-RAY DIFFRACTIONf_angle_d1.85493205
X-RAY DIFFRACTIONf_chiral_restr0.1065349
X-RAY DIFFRACTIONf_plane_restr0.0142407
X-RAY DIFFRACTIONf_dihedral_angle_d15.8353873
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.890.37641400.29731258X-RAY DIFFRACTION100
2.9-3.080.29081420.2581290X-RAY DIFFRACTION100
3.08-3.310.31021450.25241287X-RAY DIFFRACTION100
3.31-3.650.27221420.20861283X-RAY DIFFRACTION100
3.65-4.170.26831500.19551307X-RAY DIFFRACTION100
4.17-5.260.23491420.16731305X-RAY DIFFRACTION100
5.26-42.90.24431550.19721402X-RAY DIFFRACTION99.87
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)
18.005141229490.549384896709-1.347945552318.61564817903-0.7761712147877.176212217530.3793157231660.4372070174470.374343546337-0.283437838678-0.3044448462591.1720892171-0.320601454413-0.30959723555-0.06404258847760.3572391788020.0281661547178-0.05147024456510.342828312884-0.07140350206560.5108983212467.293-18.351-31.088
22.542135688210.4660835851790.02672901543141.94123613209-2.033055238862.23881793493-0.189445406067-0.0691707263091-0.0133272557330.5035020885720.598509318045-2.36281867028-0.1117495986180.198692987376-0.5890505435070.4275579739170.0613055507751-0.1075235105831.05202882671-0.4723186336870.9704265239315.351-23.557-21.402
36.291269664962.8530224712-0.721218156426.66026516780.2002998004157.073671525470.731409395316-0.7592248878380.9038583513950.771566495979-0.830955471694-0.21782665727-1.118787350981.118146959620.070361500160.693867595661-0.3783190842870.04116160094730.622011211821-0.1970279491310.68571634749717.051-7.388-21.762
45.420664243260.332061256496-1.01924122666.43763213681.198409783325.296459408241.00844311711-1.78747903210.4098678150161.96593399533-1.239514816140.933295900146-0.4284422737820.3015431141250.2749553769831.10765719438-0.5380633673880.1686095994821.1181303111-0.2847172292630.6045856755779.392-16.822-8.02
55.304930081883.55562522010.1474576674654.8645090284-0.8195416185964.197136434440.455877349152-0.854820196999-0.2091643810.551232277265-0.2449749524080.788796024137-0.4630552276780.0833591185539-0.1196671678790.421955559104-0.08713652750160.09759464955920.620076839166-0.04736275233030.3488176319452.96-27.23-19.67
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 215:291 )A215 - 291
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:5 )B1 - 5
3X-RAY DIFFRACTION3( CHAIN A AND RESID 12:72 )A12 - 72
4X-RAY DIFFRACTION4( CHAIN A AND RESID 73:164 )A73 - 164
5X-RAY DIFFRACTION5( CHAIN A AND RESID 165:214 )A165 - 214

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