[English] 日本語
Yorodumi
- PDB-5mlm: Plantago Major multifunctional oxidoreductase V150M mutant in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mlm
TitlePlantago Major multifunctional oxidoreductase V150M mutant in complex with progesterone and NADP+
ComponentsProgesterone 5-beta-reductase
KeywordsOXIDOREDUCTASE / Progesterone Reductase / Iridoid synthase / SDR / enzyme evolution
Function / homology
Function and homology information


3beta-hydroxy-Delta5-steroid dehydrogenase / 3-beta-hydroxy-delta5-steroid dehydrogenase (NAD+) activity / oxidoreductase activity, acting on the CH-CH group of donors / lipid metabolic process / nucleotide binding
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 / PROGESTERONE / Progesterone 5-beta-reductase
Similarity search - Component
Biological speciesPlantago major (common plantain)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.563 Å
AuthorsFellows, R. / Russo, C.M. / Lee, S.G. / Jez, J.M. / Chisholm, J.D. / Zubieta, C. / Nanao, M.
CitationJournal: Sci Rep / Year: 2018
Title: A multisubstrate reductase from Plantago major: structure-function in the short chain reductase superfamily.
Authors: Fellows, R. / Russo, C.M. / Silva, C.S. / Lee, S.G. / Jez, J.M. / Chisholm, J.D. / Zubieta, C. / Nanao, M.H.
History
DepositionDec 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _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 / _citation.year / _entity.formula_weight
Revision 1.2Mar 6, 2019Group: Data collection / Structure summary / Category: entity / reflns / Item: _entity.formula_weight / _reflns.pdbx_Rmerge_I_obs
Revision 1.3Jan 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: Progesterone 5-beta-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8793
Polymers46,8211
Non-polymers1,0582
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-0 kcal/mol
Surface area14570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.288, 78.288, 135.869
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Progesterone 5-beta-reductase


Mass: 46820.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plantago major (common plantain) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: D6N9X1, 3beta-hydroxy-Delta5-steroid dehydrogenase
#2: Chemical ChemComp-STR / PROGESTERONE


Mass: 314.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30O2 / Comment: hormone*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.22 Å3/Da / Density % sol: 44.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Bis Tris Propane, 5% glycerol, 16.5% to 19% Peg 5K MME

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 23, 2014 / Details: KB
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.56→50 Å / Num. obs: 25539 / % possible obs: 96.7 % / Redundancy: 4.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.91
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
5.51-504.30.02542.70.999199.4
2.56-2.652.930.8171.470.695171.5

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v6f

2v6f


Resolution: 2.563→42.914 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.22
RfactorNum. reflection% reflection
Rfree0.2577 700 5.05 %
Rwork0.1775 --
obs0.1816 13861 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.563→42.914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2912 0 71 60 3043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083074
X-RAY DIFFRACTIONf_angle_d1.0064196
X-RAY DIFFRACTIONf_dihedral_angle_d13.2411830
X-RAY DIFFRACTIONf_chiral_restr0.053445
X-RAY DIFFRACTIONf_plane_restr0.007557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.563-2.76090.37671220.30972340X-RAY DIFFRACTION89
2.7609-3.03870.3191440.2562635X-RAY DIFFRACTION100
3.0387-3.47820.30631190.20522663X-RAY DIFFRACTION100
3.4782-4.38150.21831520.15042691X-RAY DIFFRACTION100
4.3815-42.92020.23991630.14752832X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -25.0082 Å / Origin y: -12.6499 Å / Origin z: 18.1842 Å
111213212223313233
T0.3336 Å2-0.0722 Å20.0418 Å2-0.6734 Å2-0.1681 Å2--0.5213 Å2
L1.9511 °2-0.4334 °20.4872 °2-1.5593 °2-0.3743 °2--2.718 °2
S-0.021 Å °-0.7105 Å °0.1583 Å °0.1943 Å °0.008 Å °0.0233 Å °-0.3175 Å °-0.4536 Å °-0.0028 Å °
Refinement TLS groupSelection details: (chain A and resseq 26:389)

+
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