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- PDB-7y3v: Crystal structure of CdpNPT in complex with harmane -

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Basic information

Entry
Database: PDB / ID: 7y3v
TitleCrystal structure of CdpNPT in complex with harmane
ComponentsCyclic dipeptide N-prenyltransferase
KeywordsTRANSFERASE / prenyltransferases / cyclic dipeptide N-prenyltransferase
Function / homology
Function and homology information


tryptophanyl aminopeptidase / Transferases; Transferring alkyl or aryl groups, other than methyl groups / alkaloid metabolic process / prenyltransferase activity / aminopeptidase activity / proteolysis
Similarity search - Function
Aromatic prenyltransferase DMATS-type, fungi / Aromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase
Similarity search - Domain/homology
1-methyl-9H-pyrido[3,4-b]indole / PHOSPHATE ION / Cyclic dipeptide prenyltransferase
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsNakashima, Y. / Morita, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22H02777 Japan
Japan Society for the Promotion of Science (JSPS)22K15303 Japan
CitationJournal: J.Biosci.Bioeng. / Year: 2022
Title: Catalytic potential of a fungal indole prenyltransferase toward beta-carbolines, harmine and harman, and their prenylation effects on antibacterial activity.
Authors: Hamdy, S.A. / Kodama, T. / Nakashima, Y. / Han, X. / Morita, H.
History
DepositionJun 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 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: Cyclic dipeptide N-prenyltransferase
B: Cyclic dipeptide N-prenyltransferase
C: Cyclic dipeptide N-prenyltransferase
D: Cyclic dipeptide N-prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,40913
Polymers184,4674
Non-polymers9429
Water7,422412
1
A: Cyclic dipeptide N-prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4894
Polymers46,1171
Non-polymers3723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cyclic dipeptide N-prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3073
Polymers46,1171
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cyclic dipeptide N-prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3073
Polymers46,1171
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cyclic dipeptide N-prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3073
Polymers46,1171
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.655, 157.237, 161.897
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Cyclic dipeptide N-prenyltransferase


Mass: 46116.832 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: cdpNPT / Production host: Escherichia coli (E. coli) / References: UniProt: D1D8L6
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CN9 / 1-methyl-9H-pyrido[3,4-b]indole / harmane


Mass: 182.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.92 Å3/Da / Density % sol: 57.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium phosphate dibasic, 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.048 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.048 Å / Relative weight: 1
ReflectionResolution: 2.43→46.94 Å / Num. obs: 157188 / % possible obs: 100 % / Redundancy: 8.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.081 / Rrim(I) all: 0.171 / Net I/σ(I): 11.6
Reflection shellResolution: 2.43→2.48 Å / Redundancy: 8.8 % / Rmerge(I) obs: 1.049 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4449 / CC1/2: 0.778 / Rpim(I) all: 0.557 / Rrim(I) all: 1.19 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XVJ

7xvj


Resolution: 2.43→46.94 Å / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 29.9257
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2359 8233 5.24 %
Rwork0.2175 148955 -
obs0.2374 157188 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.72 Å2
Refinement stepCycle: LAST / Resolution: 2.43→46.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12553 0 0 412 12965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212865
X-RAY DIFFRACTIONf_angle_d0.495917488
X-RAY DIFFRACTIONf_chiral_restr0.03781929
X-RAY DIFFRACTIONf_plane_restr0.00372233
X-RAY DIFFRACTIONf_dihedral_angle_d16.94371718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.610.35164650.32937362X-RAY DIFFRACTION94.03
2.61-2.790.33194240.32667443X-RAY DIFFRACTION94.55
2.79-2.970.32383930.31557528X-RAY DIFFRACTION95.01
2.97-3.150.35333710.31867404X-RAY DIFFRACTION95.22
3.15-3.330.35623820.33317469X-RAY DIFFRACTION95.12
3.33-3.510.34323860.31057538X-RAY DIFFRACTION95.1
3.51-3.690.33653710.30637432X-RAY DIFFRACTION95.22
3.69-3.870.3123680.29497469X-RAY DIFFRACTION95.23
3.87-4.050.34453780.29067450X-RAY DIFFRACTION95.12
4.05-4.230.30174210.27457467X-RAY DIFFRACTION94.57
4.23-4.410.28264300.26077401X-RAY DIFFRACTION94.46
4.41-4.590.28434090.25417440X-RAY DIFFRACTION94.72
4.59-4.770.31264080.23837453X-RAY DIFFRACTION94.68
4.77-4.950.24354240.22127400X-RAY DIFFRACTION94.56
4.95-5.130.2364490.20647447X-RAY DIFFRACTION94.3
5.13-5.310.22474490.1897400X-RAY DIFFRACTION94.28
5.31-5.490.18484160.17217418X-RAY DIFFRACTION94.68
5.49-5.670.19583450.1857518X-RAY DIFFRACTION95.6
5.67-5.850.25184020.22797455X-RAY DIFFRACTION94.88
5.85-46.940.1884000.19817440X-RAY DIFFRACTION94.84

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