[English] 日本語
Yorodumi
- PDB-2hej: Crystal structure of 17alpha-hydroxysteroid dehydrogenase in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hej
TitleCrystal structure of 17alpha-hydroxysteroid dehydrogenase in complex with NADP(H) in a closed conformation
ComponentsAldo-keto reductase family 1, member C21
KeywordsOXIDOREDUCTASE / 17a-HSD / AKR1C21 / AKR / aldo-keto reductase / HSD / hydroxysteroid dehydrogenase / closed conformation
Function / homology
Function and homology information


Synthesis of bile acids and bile salts via 24-hydroxycholesterol / 17-beta-ketosteroid reductase (NADPH) activity / RA biosynthesis pathway / steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / Retinoid metabolism and transport / steroid dehydrogenase activity / 3(or 17)alpha-hydroxysteroid dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol ...Synthesis of bile acids and bile salts via 24-hydroxycholesterol / 17-beta-ketosteroid reductase (NADPH) activity / RA biosynthesis pathway / steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / Retinoid metabolism and transport / steroid dehydrogenase activity / 3(or 17)alpha-hydroxysteroid dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Prednisone ADME / 5alpha-androstane-3beta,17beta-diol dehydrogenase activity / androsterone dehydrogenase activity / ketosteroid monooxygenase activity / aldo-keto reductase (NADPH) activity / lithocholic acid binding / steroid biosynthetic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / NADP+ binding / aldose reductase (NADPH) activity / steroid metabolic process / NADPH binding / steroid binding / cytosol
Similarity search - Function
Aldo-keto reductase family 1 member C / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Chem-NDP / Aldo-keto reductase family 1 member C21 / Aldo-keto reductase family 1 member C21
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsFaucher, F. / Pereira de Jesus-Tran, K. / Cantin, L. / Luu-the, V. / Labrie, F. / Breton, R.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structures of Mouse 17alpha-Hydroxysteroid Dehydrogenase (Apoenzyme and Enzyme-NADP(H) Binary Complex): Identification of Molecular Determinants Responsible for the Unique 17alpha- ...Title: Crystal Structures of Mouse 17alpha-Hydroxysteroid Dehydrogenase (Apoenzyme and Enzyme-NADP(H) Binary Complex): Identification of Molecular Determinants Responsible for the Unique 17alpha-reductive Activity of this Enzyme.
Authors: Faucher, F. / Pereira de Jesus-Tran, K. / Cantin, L. / Luu-The, V. / Labrie, F. / Breton, R.
History
DepositionJun 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aldo-keto reductase family 1, member C21
B: Aldo-keto reductase family 1, member C21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,04313
Polymers73,8492
Non-polymers2,19411
Water13,619756
1
A: Aldo-keto reductase family 1, member C21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1158
Polymers36,9251
Non-polymers1,1907
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aldo-keto reductase family 1, member C21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9285
Polymers36,9251
Non-polymers1,0044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.500, 53.600, 86.500
Angle α, β, γ (deg.)90.00, 94.40, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Aldo-keto reductase family 1, member C21


Mass: 36924.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Akr1c21 / Plasmid: pGEX1lT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLys / References: UniProt: Q9CX32, UniProt: Q91WR5*PLUS

-
Non-polymers , 5 types, 767 molecules

#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 756 / 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: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 18% PEG-6000, 0.1M HEPES, 5% MPD, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 28, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→38.13 Å / Num. all: 142410 / Num. obs: 142410 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 17.891 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 15.88
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.35-1.40.2634.3379921348687.9
1.4-1.60.1666.61154044049992.1
1.6-1.80.07912.7749842572196.5
1.8-20.06615464111610694.5
2-2.50.05822937862134595.1
2.5-30.04930.156873950695.2
3-40.04141.641065741493.3
4-50.0350.513199263591.4
5-100.03445.712639237688.7
100.02446.2121031678.2

-
Phasing

Phasing MRRfactor: 0.362 / Cor.coef. Fo:Fc: 0.647
Highest resolutionLowest resolution
Rotation3 Å45.52 Å
Translation3 Å45.52 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
CNS1.1refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2HE8

2he8


Resolution: 1.35→38.13 Å / Rfactor Rfree error: 0.003 / FOM work R set: 0.855 / Data cutoff high absF: 1548498.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 7147 5 %RANDOM
Rwork0.201 ---
all0.201 142410 --
obs0.201 139404 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.545 Å2 / ksol: 0.385 e/Å3
Displacement parametersBiso mean: 15.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å20 Å2-0.56 Å2
2--0.89 Å20 Å2
3----2.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.35→38.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5195 0 116 780 6091
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it0.951.5
X-RAY DIFFRACTIONc_mcangle_it1.382
X-RAY DIFFRACTIONc_scbond_it1.622
X-RAY DIFFRACTIONc_scangle_it2.282.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.35-1.360.321310.28927522883
1.36-1.370.4041420.37624952637
1.37-1.380.4121240.38824482572
1.38-1.390.2881530.27827692922
1.39-1.40.2671580.24827242882
1.4-1.410.2931470.24827622909
1.41-1.420.251470.24527672914
1.42-1.430.2891480.24827552903
1.43-1.440.3211400.28526372777
1.44-1.450.2991550.29126602815
1.45-1.470.2451400.23927462886
1.47-1.480.3221250.31325022627
1.48-1.490.2291440.23127722916
1.49-1.510.2511600.22527082868
1.51-1.520.2871170.28926212738
1.52-1.540.341400.32324162556
1.54-1.550.2411510.2227842935
1.55-1.570.2391380.21627312869
1.57-1.580.2671400.21428012941
1.58-1.60.2021370.20727642901
1.6-1.620.2411560.20127802936
1.62-1.640.1981560.227712927
1.64-1.660.2121430.19627702913
1.66-1.680.211500.19527812931
1.68-1.70.2091490.19728172966
1.7-1.720.2051540.1926502804
1.72-1.750.2351400.19927302870
1.75-1.770.2251320.19428412973
1.77-1.80.221540.19627722926
1.8-1.830.2151510.19627732924
1.83-1.860.1971370.18627862923
1.86-1.90.2281260.20226862812
1.9-1.930.2741340.28225532687
1.93-1.970.2151420.19727372879
1.97-2.020.2091410.18427552896
2.02-2.060.2141540.20326752829
2.06-2.120.2961350.24625702705
2.12-2.170.1991600.18527452905
2.17-2.240.1871470.18727562903
2.24-2.310.2271300.20626882818
2.31-2.390.1991420.1927452887
2.39-2.490.2171380.18127822920
2.49-2.60.2231570.19127182875
2.6-2.740.2021270.18627122839
2.74-2.910.2021680.18627142882
2.91-3.130.1991540.18227032857
3.13-3.450.1711270.16426812808
3.45-3.950.181200.15527082828
3.95-4.970.1331590.13726222781
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ligands_.paramligands_.top
X-RAY DIFFRACTION3water_rep.paramwater.top

+
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