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- PDB-9iia: Crystal structure of the free histidine prenyltransferase FunA -

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Basic information

Entry
Database: PDB / ID: 9iia
TitleCrystal structure of the free histidine prenyltransferase FunA
ComponentsDimethylallyl tryptophan synthase GliD1
KeywordsTRANSFERASE / free histidine prenyltransferase FunA
Function / homology
Function and homology information


alkaloid metabolic process / prenyltransferase activity
Similarity search - Function
Aromatic prenyltransferase DMATS-type, fungi / Aromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase
Similarity search - Domain/homology
METHOXY-ETHOXYL / PYROPHOSPHATE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL / Dimethylallyl tryptophan synthase GliD1
Similarity search - Component
Biological speciesFusarium tricinctum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsChen, X. / Liu, Z. / Dai, S. / Zou, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)22177093 China
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Discovery, Characterization and Engineering of the Free l-Histidine C4 -Prenyltransferase.
Authors: Chen, X.W. / Liu, Z. / Dai, S. / Zou, Y.
History
DepositionJun 19, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dimethylallyl tryptophan synthase GliD1
B: Dimethylallyl tryptophan synthase GliD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,3777
Polymers98,6182
Non-polymers7595
Water1,892105
1
A: Dimethylallyl tryptophan synthase GliD1
hetero molecules

A: Dimethylallyl tryptophan synthase GliD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,3026
Polymers98,6182
Non-polymers6844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/21
Buried area3470 Å2
ΔGint-34 kcal/mol
Surface area31800 Å2
MethodPISA
2
B: Dimethylallyl tryptophan synthase GliD1
hetero molecules

B: Dimethylallyl tryptophan synthase GliD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4528
Polymers98,6182
Non-polymers8356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/21
Buried area3900 Å2
ΔGint-50 kcal/mol
Surface area32500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.210, 202.210, 111.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11B-656-

HOH

21B-657-

HOH

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Components

#1: Protein Dimethylallyl tryptophan synthase GliD1


Mass: 49308.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: According to the author, the FunA gene was from Fusarium tricinctum CGMCC 3.4731 sourced from China General Microbiological Culture Collection Center (CGMCC). Thus, the FunA sequence is ...Details: According to the author, the FunA gene was from Fusarium tricinctum CGMCC 3.4731 sourced from China General Microbiological Culture Collection Center (CGMCC). Thus, the FunA sequence is different from reference sequence (A0A8K0WD55).
Source: (gene. exp.) Fusarium tricinctum (fungus) / Strain: Fusarium tricinctum CGMCC 3.4731 / Gene: BKA59DRAFT_455755 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8K0WD55
#2: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4O7P2
#3: Chemical ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16O4
#4: Chemical ChemComp-MOE / METHOXY-ETHOXYL


Mass: 75.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.32 Å3/Da / Density % sol: 62.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 1.5 M ammonium sulfate, 0.1 M BIS-TRIS pH 6.5, 2% v/v polyethylene glycol monomethyl ether 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.27→31.48 Å / Num. obs: 61921 / % possible obs: 100 % / Redundancy: 42.3 % / CC1/2: 0.999 / Net I/σ(I): 24
Reflection shellResolution: 2.27→2.33 Å / Redundancy: 37.2 % / Num. unique obs: 4522 / CC1/2: 0.616

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→31.45 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2522 1999 3.23 %
Rwork0.2134 --
obs0.2147 61808 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.27→31.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6632 0 0 105 6737
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086833
X-RAY DIFFRACTIONf_angle_d1.039293
X-RAY DIFFRACTIONf_dihedral_angle_d7.628942
X-RAY DIFFRACTIONf_chiral_restr0.0551004
X-RAY DIFFRACTIONf_plane_restr0.0081188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.330.2951400.27584209X-RAY DIFFRACTION100
2.33-2.390.32741400.26184168X-RAY DIFFRACTION100
2.39-2.460.28591410.24574221X-RAY DIFFRACTION100
2.46-2.540.31811410.24184215X-RAY DIFFRACTION100
2.54-2.630.28531410.23784211X-RAY DIFFRACTION100
2.63-2.740.29291410.23384222X-RAY DIFFRACTION100
2.74-2.860.321420.23554231X-RAY DIFFRACTION100
2.86-3.010.24861420.23364255X-RAY DIFFRACTION100
3.01-3.20.25211420.22694254X-RAY DIFFRACTION100
3.2-3.450.28111420.22324269X-RAY DIFFRACTION100
3.45-3.790.24161440.21344284X-RAY DIFFRACTION100
3.79-4.340.23781440.18954320X-RAY DIFFRACTION100
4.34-5.460.21761460.17964377X-RAY DIFFRACTION100
5.46-31.450.24041530.21964573X-RAY DIFFRACTION100

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