[English] 日本語
Yorodumi
- PDB-7ve7: Crystal structure of KRED mutant-F147L/L153Q/Y190P/L199A/M205F/M206F -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ve7
TitleCrystal structure of KRED mutant-F147L/L153Q/Y190P/L199A/M205F/M206F
Components3-alpha-(Or 20-beta)-hydroxysteroid dehydrogenase
KeywordsOXIDOREDUCTASE / Ketoreductases / NADPH-dependent / Enantioselectivity
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity / nucleotide binding / metal ion binding
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADP-dependent (R)-specific alcohol dehydrogenase
Similarity search - Component
Biological speciesLactobacillus kefiri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72000696882 Å
AuthorsCui, J. / Huang, X. / Wang, B. / Zhao, H. / Zhou, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Catal / Year: 2022
Title: Photoinduced chemomimetic biocatalysis for enantioselective intermolecular radical conjugate addition
Authors: Huang, X. / Feng, J. / Cui, J. / Jiang, G. / Harrison, W. / Zang, X. / Zhou, J. / Wang, B. / Zhao, H.
History
DepositionSep 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 11, 2022Provider: 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: 3-alpha-(Or 20-beta)-hydroxysteroid dehydrogenase
B: 3-alpha-(Or 20-beta)-hydroxysteroid dehydrogenase
C: 3-alpha-(Or 20-beta)-hydroxysteroid dehydrogenase
D: 3-alpha-(Or 20-beta)-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,11510
Polymers107,0934
Non-polymers3,0226
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, It was already revealed that KRED are tetramers(pdb:4rf2). The sequence homology between P2-D12-2a and KRED in their paper are higher than 90%.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19140 Å2
ΔGint-107 kcal/mol
Surface area29570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.310, 55.570, 128.560
Angle α, β, γ (deg.)90.000, 103.890, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein
3-alpha-(Or 20-beta)-hydroxysteroid dehydrogenase / NADPH dependent R-specific alcohol dehydrogenase / SDR family NAD(P)-dependent oxidoreductase


Mass: 26773.164 Da / Num. of mol.: 4 / Mutation: F147L,L153Q,Y190P,L199A,M205F,M206F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus kefiri (bacteria) / Gene: adhR, fabG3, DNL43_05835, LKE01_04370
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q6WVP7
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.09 Å3/Da / Density % sol: 41.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris pH 6.5, 25% (w/v) PEG3350, 0.2 M MgCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97919 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.72→23.84 Å / Num. obs: 93405 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 29.5105622665 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.028 / Rrim(I) all: 0.071 / Net I/σ(I): 13.9
Reflection shellResolution: 1.72→1.76 Å / Redundancy: 7 % / Rmerge(I) obs: 1.018 / Num. unique obs: 6873 / CC1/2: 0.836 / Rpim(I) all: 0.413 / Rrim(I) all: 1.1 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RF2

4rf2


Resolution: 1.72000696882→21.3270754494 Å / SU ML: 0.192447001479 / Cross valid method: FREE R-VALUE / σ(F): 1.34760516911 / Phase error: 24.5983880853
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.209694417468 4703 5.03970252575 %
Rwork0.173649289 88616 -
obs0.175432672799 93319 99.6359171471 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.1814740486 Å2
Refinement stepCycle: LAST / Resolution: 1.72000696882→21.3270754494 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7414 0 194 372 7980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005349298820697752
X-RAY DIFFRACTIONf_angle_d0.91294191678610547
X-RAY DIFFRACTIONf_chiral_restr0.0584684533991216
X-RAY DIFFRACTIONf_plane_restr0.004661284474591350
X-RAY DIFFRACTIONf_dihedral_angle_d10.27595347444937
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.720007-1.73950.354623063141440.3098457591052979X-RAY DIFFRACTION99.8401534527
1.7395-1.760.3459355636771780.2913977377572911X-RAY DIFFRACTION99.8383968972
1.76-1.78150.3091770376951620.2886831557452928X-RAY DIFFRACTION99.6774193548
1.7815-1.8040.2566554601781590.2650103114862912X-RAY DIFFRACTION99.6754300552
1.804-1.82770.2911933244651480.2392807500022942X-RAY DIFFRACTION100
1.8277-1.85270.2678017651811490.2463528553462975X-RAY DIFFRACTION99.968
1.8527-1.87920.2780185030761410.2330982651292942X-RAY DIFFRACTION99.8380829016
1.8792-1.90720.2289875883731460.2180986492182966X-RAY DIFFRACTION99.8075689545
1.9072-1.9370.2202036507061500.2209023954092917X-RAY DIFFRACTION99.7398373984
1.937-1.96870.2482381296791790.203186576172941X-RAY DIFFRACTION99.935938501
1.9687-2.00270.2591013461221670.1997854982922962X-RAY DIFFRACTION99.8404594767
2.0027-2.03910.239551903891570.1960362285872922X-RAY DIFFRACTION99.7408487204
2.0391-2.07820.2495833475571270.1978387727182961X-RAY DIFFRACTION99.8706338939
2.0782-2.12060.1983408506561580.1801953642032986X-RAY DIFFRACTION100
2.1206-2.16670.2083484021931770.1791261770282889X-RAY DIFFRACTION99.9348109518
2.1667-2.2170.203050922641470.1691071670152972X-RAY DIFFRACTION99.6485623003
2.217-2.27240.2010629544851560.1731888634432925X-RAY DIFFRACTION99.6764801035
2.2724-2.33380.2198601773651580.1743344697013008X-RAY DIFFRACTION99.8738170347
2.3338-2.40240.2051472738551650.1659516391042937X-RAY DIFFRACTION99.8390730608
2.4024-2.47980.2168071329671560.1783071809042914X-RAY DIFFRACTION99.8698763826
2.4798-2.56830.2078862341161650.1800029997042969X-RAY DIFFRACTION99.7136493796
2.5683-2.67090.2158291635171490.1801347314722953X-RAY DIFFRACTION99.7748472178
2.6709-2.79230.2230541405411590.1892887521752983X-RAY DIFFRACTION99.2733017378
2.7923-2.93910.2237213336261570.1831712104012934X-RAY DIFFRACTION99.3890675241
2.9391-3.12270.2099653658151750.188542968712926X-RAY DIFFRACTION99.4228919525
3.1227-3.3630.2458910094391430.1719901583422961X-RAY DIFFRACTION99.4871794872
3.363-3.69980.1867176380711590.1538732270822994X-RAY DIFFRACTION99.0574929312
3.6998-4.23160.18233265451580.1454827489752946X-RAY DIFFRACTION98.8535031847
4.2316-5.31760.1744242768311740.1412207980182993X-RAY DIFFRACTION99.5285983658
5.3176-21.30.1983609690321400.1645589194533068X-RAY DIFFRACTION98.1940618304
Refinement TLS params.Method: refined / Origin x: 30.8350315932 Å / Origin y: -31.6108450183 Å / Origin z: 31.0434383873 Å
111213212223313233
T0.191689551857 Å2-0.0204709441846 Å2-0.0224162348247 Å2-0.175091424909 Å20.00105044069686 Å2--0.213165875631 Å2
L1.08182630806 °2-0.0218818003386 °2-0.604342815628 °2-1.4166475292 °2-0.136316732208 °2--1.90601210293 °2
S0.0333578252224 Å °0.00713645077027 Å °-0.0230439169052 Å °-0.0462023147831 Å °-0.0567266628262 Å °-0.0885509638302 Å °-0.0161225574775 Å °0.150738988522 Å °0.0184571529957 Å °
Refinement TLS groupSelection details: all

+
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