[English] 日本語
Yorodumi
- PDB-6el3: Structure of Progesterone 5beta-Reductase from Arabidopsis thalia... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6el3
TitleStructure of Progesterone 5beta-Reductase from Arabidopsis thaliana in complex with NADP
Components(3-oxo-Delta(4,5)-steroid 5-beta- ...) x 6
KeywordsOXIDOREDUCTASE / short chain dehydrogenase/reductase (SDR) fold / homodimer / NADP binding site
Function / homology
Function and homology information


enone reductase activity / Delta4-3-oxosteroid 5beta-reductase / xylem and phloem pattern formation / Delta4-3-oxosteroid 5beta-reductase activity / steroid metabolic process / response to wounding / protein dimerization activity / cytosol
Similarity search - Function
PRISE-like Rossmann-fold domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 3-oxo-Delta(4,5)-steroid 5-beta-reductase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 Å
AuthorsMuller, Y.A. / Schmidt, K. / Egerer-Sieber, C.
CitationJournal: Phytochemistry / Year: 2018
Title: PRISEs (progesterone 5 beta-reductase and/or iridoid synthase-like 1,4-enone reductases): Catalytic and substrate promiscuity allows for realization of multiple pathways in plant metabolism.
Authors: Schmidt, K. / Petersen, J. / Munkert, J. / Egerer-Sieber, C. / Hornig, M. / Muller, Y.A. / Kreis, W.
History
DepositionSep 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-oxo-Delta(4,5)-steroid 5-beta-reductase
B: 3-oxo-Delta(4,5)-steroid 5-beta-reductase
C: 3-oxo-Delta(4,5)-steroid 5-beta-reductase
D: 3-oxo-Delta(4,5)-steroid 5-beta-reductase
E: 3-oxo-Delta(4,5)-steroid 5-beta-reductase
F: 3-oxo-Delta(4,5)-steroid 5-beta-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,90118
Polymers264,2286
Non-polymers4,67312
Water48,1542673
1
C: 3-oxo-Delta(4,5)-steroid 5-beta-reductase
D: 3-oxo-Delta(4,5)-steroid 5-beta-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6166
Polymers88,0582
Non-polymers1,5584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-47 kcal/mol
Surface area29160 Å2
MethodPISA
2
E: 3-oxo-Delta(4,5)-steroid 5-beta-reductase
F: 3-oxo-Delta(4,5)-steroid 5-beta-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5896
Polymers88,0312
Non-polymers1,5584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-48 kcal/mol
Surface area28990 Å2
MethodPISA
3
A: 3-oxo-Delta(4,5)-steroid 5-beta-reductase
B: 3-oxo-Delta(4,5)-steroid 5-beta-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6976
Polymers88,1392
Non-polymers1,5584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-47 kcal/mol
Surface area29150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.460, 94.860, 313.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
3-oxo-Delta(4,5)-steroid 5-beta- ... , 6 types, 6 molecules ABCDEF

#1: Protein 3-oxo-Delta(4,5)-steroid 5-beta-reductase / Delta(4)-3-oxosteroid 5-beta-reductase / Delta-4 / 5-steroid 5-beta-reductase / At5beta-StR / ...Delta(4)-3-oxosteroid 5-beta-reductase / Delta-4 / 5-steroid 5-beta-reductase / At5beta-StR / Progesterone 5-beta-reductase / 5beta-POR / Protein VEIN PATTERNING 1


Mass: 44055.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: -N-terminal residues were not modelled due to missing electron density -Dimethyllysines were only built where electron density was unambiguous
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VEP1, AWI31, At4g24220, T22A6.50 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9STX2, Delta4-3-oxosteroid 5beta-reductase
#2: Protein 3-oxo-Delta(4,5)-steroid 5-beta-reductase / Delta(4)-3-oxosteroid 5-beta-reductase / Delta-4 / 5-steroid 5-beta-reductase / At5beta-StR / ...Delta(4)-3-oxosteroid 5-beta-reductase / Delta-4 / 5-steroid 5-beta-reductase / At5beta-StR / Progesterone 5-beta-reductase / 5beta-POR / Protein VEIN PATTERNING 1


Mass: 44083.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: -N-terminal residues were not modelled due to missing electron density -Dimethyllysines were only built where electron density was unambiguous
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VEP1, AWI31, At4g24220, T22A6.50 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9STX2, Delta4-3-oxosteroid 5beta-reductase
#3: Protein 3-oxo-Delta(4,5)-steroid 5-beta-reductase / Delta(4)-3-oxosteroid 5-beta-reductase / Delta-4 / 5-steroid 5-beta-reductase / At5beta-StR / ...Delta(4)-3-oxosteroid 5-beta-reductase / Delta-4 / 5-steroid 5-beta-reductase / At5beta-StR / Progesterone 5-beta-reductase / 5beta-POR / Protein VEIN PATTERNING 1


Mass: 44055.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: -N-terminal residues were not modelled due to missing electron density -Dimethyllysines were only built where electron density was unambiguous
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VEP1, AWI31, At4g24220, T22A6.50 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9STX2, Delta4-3-oxosteroid 5beta-reductase
#4: Protein 3-oxo-Delta(4,5)-steroid 5-beta-reductase / Delta(4)-3-oxosteroid 5-beta-reductase / Delta-4 / 5-steroid 5-beta-reductase / At5beta-StR / ...Delta(4)-3-oxosteroid 5-beta-reductase / Delta-4 / 5-steroid 5-beta-reductase / At5beta-StR / Progesterone 5-beta-reductase / 5beta-POR / Protein VEIN PATTERNING 1


Mass: 44001.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: -N-terminal residues were not modelled due to missing electron density -Dimethyllysines were only built where electron density was unambiguous
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VEP1, AWI31, At4g24220, T22A6.50 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9STX2, Delta4-3-oxosteroid 5beta-reductase
#5: Protein 3-oxo-Delta(4,5)-steroid 5-beta-reductase / Delta(4)-3-oxosteroid 5-beta-reductase / Delta-4 / 5-steroid 5-beta-reductase / At5beta-StR / ...Delta(4)-3-oxosteroid 5-beta-reductase / Delta-4 / 5-steroid 5-beta-reductase / At5beta-StR / Progesterone 5-beta-reductase / 5beta-POR / Protein VEIN PATTERNING 1


Mass: 44055.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: -N-terminal residues were not modelled due to missing electron density -Dimethyllysines were only built where electron density was unambiguous
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VEP1, AWI31, At4g24220, T22A6.50 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9STX2, Delta4-3-oxosteroid 5beta-reductase
#6: Protein 3-oxo-Delta(4,5)-steroid 5-beta-reductase / Delta(4)-3-oxosteroid 5-beta-reductase / Delta-4 / 5-steroid 5-beta-reductase / At5beta-StR / ...Delta(4)-3-oxosteroid 5-beta-reductase / Delta-4 / 5-steroid 5-beta-reductase / At5beta-StR / Progesterone 5-beta-reductase / 5beta-POR / Protein VEIN PATTERNING 1


Mass: 43974.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: -N-terminal residues were not modelled due to missing electron density -Dimethyllysines were only built where electron density was unambiguous
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VEP1, AWI31, At4g24220, T22A6.50 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9STX2, Delta4-3-oxosteroid 5beta-reductase

-
Non-polymers , 3 types, 2685 molecules

#7: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2673 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2 / Details: 1.4 M sodium potassium phosphate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.899→47.43 Å / Num. obs: 217162 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.996 / Rrim(I) all: 0.169 / Net I/σ(I): 9.35
Reflection shellResolution: 1.899→2.01 Å / Redundancy: 6.9 % / Num. unique obs: 34610 / CC1/2: 0.731 / Rrim(I) all: 0.93 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V6G

2v6g


Resolution: 1.899→46.896 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.51
RfactorNum. reflection% reflection
Rfree0.2128 2280 1.05 %
Rwork0.1675 --
obs0.168 217118 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.899→46.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17740 0 294 2673 20707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818594
X-RAY DIFFRACTIONf_angle_d1.125350
X-RAY DIFFRACTIONf_dihedral_angle_d21.1626728
X-RAY DIFFRACTIONf_chiral_restr0.6082647
X-RAY DIFFRACTIONf_plane_restr0.0053206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.899-1.94030.28781390.236213094X-RAY DIFFRACTION98
1.9403-1.98550.26491410.217913254X-RAY DIFFRACTION100
1.9855-2.03510.22191420.205213374X-RAY DIFFRACTION100
2.0351-2.09010.25031410.194313287X-RAY DIFFRACTION100
2.0901-2.15170.24871420.19213361X-RAY DIFFRACTION100
2.1517-2.22110.22751410.180413323X-RAY DIFFRACTION100
2.2211-2.30050.23111420.178613339X-RAY DIFFRACTION100
2.3005-2.39260.21361420.170113387X-RAY DIFFRACTION100
2.3926-2.50150.19171420.168813420X-RAY DIFFRACTION100
2.5015-2.63330.22411420.172713403X-RAY DIFFRACTION100
2.6333-2.79830.24671430.176813434X-RAY DIFFRACTION100
2.7983-3.01430.22411420.182213426X-RAY DIFFRACTION100
3.0143-3.31760.23081430.169413480X-RAY DIFFRACTION100
3.3176-3.79750.18281430.151213566X-RAY DIFFRACTION100
3.7975-4.78370.15921450.130513651X-RAY DIFFRACTION100
4.7837-46.91070.20491500.148414039X-RAY DIFFRACTION99

+
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