[English] 日本語
Yorodumi
- PDB-3uyi: Crystal Structure of Perakine Reductase, Founder Member of a Nove... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3uyi
TitleCrystal Structure of Perakine Reductase, Founder Member of a Novel AKR Subfamily with Unique Conformational Changes during NADPH Binding
ComponentsPerakine reductase
KeywordsOXIDOREDUCTASE / AKR superfamily / 8/6 barrel / Perakine Reductase / NADPH
Function / homology
Function and homology information


perakine reductase / alkaloid metabolic process / aldo-keto reductase (NADPH) activity / cytoplasm
Similarity search - Function
: / NADP-dependent oxidoreductase domain / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesRauvolfia serpentina (serpentwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.313 Å
AuthorsSun, L. / Chen, Y. / Rajendran, C. / Panjikar, S. / Mueller, U. / Wang, M. / Rosenthal, C. / Mindnich, R. / Penning, T.M. / Stoeckigt, J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal structure of perakine reductase, founding member of a novel aldo-keto reductase (AKR) subfamily that undergoes unique conformational changes during NADPH binding.
Authors: Sun, L. / Chen, Y. / Rajendran, C. / Mueller, U. / Panjikar, S. / Wang, M. / Mindnich, R. / Rosenthal, C. / Penning, T.M. / Stockigt, J.
History
DepositionDec 6, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Perakine reductase


Theoretical massNumber of molelcules
Total (without water)37,2301
Polymers37,2301
Non-polymers00
Water88349
1
A: Perakine reductase

A: Perakine reductase


Theoretical massNumber of molelcules
Total (without water)74,4592
Polymers74,4592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5640 Å2
ΔGint-32 kcal/mol
Surface area27270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.802, 93.047, 143.011
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Perakine reductase


Mass: 37229.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rauvolfia serpentina (serpentwood) / Gene: PR / Production host: Escherichia coli (E. coli) / References: UniProt: Q3L181
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.2 %

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.313→40 Å / Num. obs: 20584 / % possible obs: 95.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PZ0

1pz0


Resolution: 2.313→19.799 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8167 / SU ML: 0.34 / σ(F): 1.35 / σ(I): 2 / Phase error: 23.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 932 5.5 %Random
Rwork0.1892 ---
obs0.1918 16946 96.77 %-
all-20584 --
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.339 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 158.2 Å2 / Biso min: 24.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.595 Å20 Å2-0 Å2
2--0.6573 Å20 Å2
3----1.2524 Å2
Refinement stepCycle: LAST / Resolution: 2.313→19.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2427 0 0 49 2476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152473
X-RAY DIFFRACTIONf_angle_d1.5133343
X-RAY DIFFRACTIONf_dihedral_angle_d14.337927
X-RAY DIFFRACTIONf_chiral_restr0.079383
X-RAY DIFFRACTIONf_plane_restr0.008426
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.313-2.43470.28961300.237216393
2.4347-2.5870.30081280.2422223496
2.587-2.78620.29581260.2323223395
2.7862-3.06570.31371450.2053224296
3.0657-3.50720.23931340.2064230198
3.5072-4.41060.21511380.1676236399
4.4106-19.79940.20011310.1721247899
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)
12.55410.7276-0.86982.86590.90483.71550.2375-0.43410.19390.35880.0678-0.34920.60190.6845-0.34010.36630.0191-0.02940.3635-0.04630.40268.350426.249561.307
22.75530.02940.96471.6268-0.23232.94840.02450.3789-0.0873-0.1551-0.0153-0.46010.41740.8952-0.13640.3390.07950.05510.4543-0.05660.470814.310422.545853.3382
32.73210.1130.13551.4554-0.21413.21260.22640.1205-0.2404-0.099-0.0381-0.03010.6514-0.1551-0.18610.4059-0.0251-0.02660.24920.00560.3379-1.567116.575854.2451
42.64030.9751.00144.2682-1.18833.0468-0.0260.18740.383-0.12060.07820.5455-0.0105-0.27010.14110.25470.00270.03910.3930.0350.3343-6.506835.167159.1459
50.75950.65530.51540.79611.07032.32430.1783-1.36420.45760.4877-0.2574-0.1504-0.45750.09560.30270.5879-0.0920.07590.911-0.22140.49514.179537.686338.0166
63.1099-0.28720.39522.4660.11542.0373-0.20870.31340.0875-0.08620.1296-0.274-0.39510.45550.06620.4158-0.14590.00470.4181-0.05810.32429.827242.81157.802
71.3312-0.04070.85941.58761.68994.2915-0.05340.278-0.1352-0.7975-0.0946-0.1001-0.8477-0.75450.05650.70360.02130.03620.5861-0.0660.4065-1.694847.34455.7677
80.61860.2352-0.52612.24660.56792.82650.319-0.2901-0.49770.0934-0.28560.0697-0.58290.4569-0.01040.4107-0.001-0.00610.5536-0.05810.637113.293129.432824.3167
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 0:32)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 33:61)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 62:178)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 179:204)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 205:241)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 242:294)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 295:321)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 322:336)

+
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