[English] 日本語
Yorodumi
- PDB-6s5u: Strictosidine Synthase from Ophiorrhiza pumila in complex with N-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6s5u
TitleStrictosidine Synthase from Ophiorrhiza pumila in complex with N-[2-(1H-Indol-3-yl)ethyl]-3-methyl-1-butanamine
ComponentsStrictosidine synthase
KeywordsLYASE / alkaloid / C-C bond / Pictet-Spenglerase
Function / homology
Function and homology information


vacuole / endomembrane system / hydrolase activity
Similarity search - Function
Strictosidine synthase-like, N-terminal / Strictosidine synthase, conserved region / Strictosidine synthase / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Chem-KWK / Strictosidine synthase
Similarity search - Component
Biological speciesOphiorrhiza pumila (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsEger, E. / Sharma, M. / Kroutil, W. / Grogan, G.
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Inverted Binding of Non-natural Substrates in Strictosidine Synthase Leads to a Switch of Stereochemical Outcome in Enzyme-Catalyzed Pictet-Spengler Reactions.
Authors: Eger, E. / Simon, A. / Sharma, M. / Yang, S. / Breukelaar, W.B. / Grogan, G. / Houk, K.N. / Kroutil, W.
History
DepositionJul 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Strictosidine synthase
C: Strictosidine synthase
B: Strictosidine synthase
D: Strictosidine synthase
E: Strictosidine synthase
F: Strictosidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,61419
Polymers220,6196
Non-polymers2,99513
Water12,809711
1
A: Strictosidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2313
Polymers36,7701
Non-polymers4612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Strictosidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2313
Polymers36,7701
Non-polymers4612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Strictosidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4614
Polymers36,7701
Non-polymers6913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Strictosidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2313
Polymers36,7701
Non-polymers4612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Strictosidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2313
Polymers36,7701
Non-polymers4612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Strictosidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2313
Polymers36,7701
Non-polymers4612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.747, 125.747, 117.081
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22B
13A
23D
14A
24E
15A
25F
16C
26B
17C
27D
18C
28E
19C
29F
110B
210D
111B
211E
112B
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROTYRTYRAA5 - 3045 - 304
21PROPROTYRTYRCB5 - 3045 - 304
12SERSERTYRTYRAA4 - 3044 - 304
22SERSERTYRTYRBC4 - 3044 - 304
13PROPROTYRTYRAA5 - 3045 - 304
23PROPROTYRTYRDD5 - 3045 - 304
14PROPROASNASNAA5 - 3035 - 303
24PROPROASNASNEE5 - 3035 - 303
15PROPROTYRTYRAA5 - 3045 - 304
25PROPROTYRTYRFF5 - 3045 - 304
16PROPROASNASNCB5 - 3035 - 303
26PROPROASNASNBC5 - 3035 - 303
17PROPROLYSLYSCB5 - 3055 - 305
27PROPROLYSLYSDD5 - 3055 - 305
18PROPROASNASNCB5 - 3035 - 303
28PROPROASNASNEE5 - 3035 - 303
19PROPROLYSLYSCB5 - 3055 - 305
29PROPROLYSLYSFF5 - 3055 - 305
110PROPROASNASNBC5 - 3035 - 303
210PROPROASNASNDD5 - 3035 - 303
111PROPROTYRTYRBC5 - 3045 - 304
211PROPROTYRTYREE5 - 3045 - 304
112PROPROASNASNBC5 - 3035 - 303
212PROPROASNASNFF5 - 3035 - 303
113PROPROASNASNDD5 - 3035 - 303
213PROPROASNASNEE5 - 3035 - 303
114PROPROLYSLYSDD5 - 3055 - 305
214PROPROLYSLYSFF5 - 3055 - 305
115PROPROASNASNEE5 - 3035 - 303
215PROPROASNASNFF5 - 3035 - 303

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

-
Components

#1: Protein
Strictosidine synthase


Mass: 36769.902 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ophiorrhiza pumila (plant) / Gene: str / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Shuffle / References: UniProt: Q94LW9
#2: Chemical
ChemComp-KWK / ~{N}-[2-(1~{H}-indol-3-yl)ethyl]-3-methyl-butan-1-amine


Mass: 230.349 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C15H22N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 711 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% PEG 6000; 0.3 M MH4Cl; 0.1M Tris-HCl pH 8.0

-
Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.03→39.9 Å / Num. obs: 133410 / % possible obs: 99.7 % / Redundancy: 5.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.12 / Net I/σ(I): 6.8
Reflection shellResolution: 2.03→2.06 Å / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 6658 / CC1/2: 0.97 / Rpim(I) all: 0.44

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FP9

2fp9


Resolution: 2.03→39.9 Å / Cor.coef. Fo:Fc: 0.815 / Cor.coef. Fo:Fc free: 0.787 / SU B: 9.408 / SU ML: 0.261 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.304 / ESU R Free: 0.237
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3338 6605 5 %RANDOM
Rwork0.3119 ---
obs0.313 126761 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 139.47 Å2 / Biso mean: 16.832 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å2-0.59 Å2-0 Å2
2---1.18 Å2-0 Å2
3---3.84 Å2
Refinement stepCycle: final / Resolution: 2.03→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13970 0 221 711 14902
Biso mean--6.26 18.22 -
Num. residues----1805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01314613
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712891
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.63719891
X-RAY DIFFRACTIONr_angle_other_deg1.1771.57229766
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.62251808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.91922.902758
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.091152072
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5651564
X-RAY DIFFRACTIONr_chiral_restr0.0630.21835
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216772
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023322
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A92790.05
12C92790.05
21A92320.05
22B92320.05
31A92850.05
32D92850.05
41A92220.05
42E92220.05
51A92510.06
52F92510.06
61C91430.05
62B91430.05
71C92260.06
72D92260.06
81C91920.05
82E91920.05
91C92120.06
92F92120.06
101B91420.05
102D91420.05
111B91290.06
112E91290.06
121B91860.05
122F91860.05
131D92410.05
132E92410.05
141D93550.04
142F93550.04
151E92110.05
152F92110.05
LS refinement shellResolution: 2.03→2.083 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 418 -
Rwork0.345 9470 -
all-9888 -
obs--100 %

+
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