[English] 日本語
Yorodumi
- PDB-7y3v: Crystal structure of CdpNPT in complex with harmane -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Comment: alkaloid*YM
#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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more