[English] 日本語
Yorodumi
- PDB-5js6: Crystal structure of 17beta-hydroxysteroid dehydrogenase 14 T205 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5js6
TitleCrystal structure of 17beta-hydroxysteroid dehydrogenase 14 T205 variant in complex with NAD.
Components17-beta-hydroxysteroid dehydrogenase 14
KeywordsOXIDOREDUCTASE / cofactor complex / hydroxysteroid dehydrogenase
Function / homology
Function and homology information


Estrogen biosynthesis / testosterone 17-beta-dehydrogenase (NADP+) activity / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / steroid catabolic process / identical protein binding / cytosol
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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / TRIETHYLENE GLYCOL / 17-beta-hydroxysteroid dehydrogenase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
AuthorsBertoletti, N. / Marchais-Oberwinkler, S. / Heine, A. / Klebe, G.
Funding support2items
OrganizationGrant numberCountry
German Research FoundationMA-5287/1-1
German Research FoundationKL-1204/15-1
CitationJournal: J.Med.Chem. / Year: 2016
Title: New Insights into Human 17 beta-Hydroxysteroid Dehydrogenase Type 14: First Crystal Structures in Complex with a Steroidal Ligand and with a Potent Nonsteroidal Inhibitor.
Authors: Bertoletti, N. / Braun, F. / Lepage, M. / Moller, G. / Adamski, J. / Heine, A. / Klebe, G. / Marchais-Oberwinkler, S.
History
DepositionMay 7, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 17-beta-hydroxysteroid dehydrogenase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7265
Polymers28,6831
Non-polymers1,0434
Water1,15364
1
A: 17-beta-hydroxysteroid dehydrogenase 14
hetero molecules

A: 17-beta-hydroxysteroid dehydrogenase 14
hetero molecules

A: 17-beta-hydroxysteroid dehydrogenase 14
hetero molecules

A: 17-beta-hydroxysteroid dehydrogenase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,90420
Polymers114,7314
Non-polymers4,17316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area25820 Å2
ΔGint-208 kcal/mol
Surface area33110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.206, 130.206, 130.206
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-303-

PG4

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein 17-beta-hydroxysteroid dehydrogenase 14 / 17-beta-HSD 14 / 17-beta-hydroxysteroid dehydrogenase DHRS10 / Dehydrogenase/reductase SDR family ...17-beta-HSD 14 / 17-beta-hydroxysteroid dehydrogenase DHRS10 / Dehydrogenase/reductase SDR family member 10 / Retinal short-chain dehydrogenase/reductase retSDR3 / Short chain dehydrogenase/reductase family 47C member 1


Mass: 28682.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B14, DHRS10, SDR3, SDR47C1, UNQ502/PRO474 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: Q9BPX1, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor

-
Non-polymers , 5 types, 68 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: HEPES 0.1 M pH 7.00, sodium formate 3.3 M / PH range: 7-8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 24734 / % possible obs: 99.4 % / Redundancy: 6.62 % / Rsym value: 0.04 / Net I/σ(I): 20.98
Reflection shellResolution: 2→2.12 Å / Redundancy: 6.52 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 3.91 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: 000)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EN4

5en4


Resolution: 2.002→46.035 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.69
RfactorNum. reflection% reflection
Rfree0.1907 1237 5 %
Rwork0.1661 --
obs0.1674 24731 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.002→46.035 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1939 0 62 64 2065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072036
X-RAY DIFFRACTIONf_angle_d0.8172777
X-RAY DIFFRACTIONf_dihedral_angle_d19.4611230
X-RAY DIFFRACTIONf_chiral_restr0.053325
X-RAY DIFFRACTIONf_plane_restr0.005382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.002-2.08210.32131340.27662546X-RAY DIFFRACTION98
2.0821-2.17690.25811370.21412598X-RAY DIFFRACTION100
2.1769-2.29170.26131370.21122612X-RAY DIFFRACTION100
2.2917-2.43520.24291360.20212581X-RAY DIFFRACTION100
2.4352-2.62330.23041380.18882619X-RAY DIFFRACTION99
2.6233-2.88720.20721380.17662619X-RAY DIFFRACTION100
2.8872-3.30490.1991360.17542587X-RAY DIFFRACTION99
3.3049-4.16340.16311390.1522644X-RAY DIFFRACTION100
4.1634-46.04690.16561420.14382688X-RAY DIFFRACTION99
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)
14.19420.0075-0.4210.73411.32412.4369-0.1750.24120.1334-0.0772-0.1429-0.5508-0.31820.69560.22650.3889-0.04230.19110.52930.21360.963726.65553.733747.9463
22.93910.1374-0.13981.391-0.41021.5346-0.28780.57150.045-0.455-0.1521-0.57340.04040.33710.33440.4572-0.00090.18780.42510.15320.781817.01261.625841.3164
36.6103-5.0342.58855.1078-1.93312.5084-0.15720.6828-0.1025-0.4404-0.3274-0.5120.0480.37470.46340.3869-0.02270.13790.34540.03980.68739.9743-3.976342.2779
42.65580.3732-0.10112.70161.09712.3615-0.34540.14110.2126-0.344-0.0075-0.2567-0.06860.10240.32820.292-0.03950.03260.29490.08270.6677.90873.618254.0253
51.0436-0.05160.19763.0894-0.47921.4623-0.11410.0971-0.1318-0.2703-0.1973-0.2647-0.03170.07740.32050.3177-0.00870.03240.35420.06770.69119.31554.60952.011
60.2489-0.3078-0.53942.9435-0.03481.3152-0.1154-0.0732-0.0754-0.0831-0.1707-0.5286-0.16690.24580.27640.302-0.0405-0.07060.35440.11450.821614.05329.503461.1385
74.02-0.1572-2.92614.5293-0.05393.30790.0550.45140.7253-0.09370.05660.5316-0.721-0.5492-0.10930.5869-0.005-0.10130.5048-0.03140.8887-10.441322.032765.5373
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 52 )
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 103 )
3X-RAY DIFFRACTION3chain 'A' and (resid 104 through 132 )
4X-RAY DIFFRACTION4chain 'A' and (resid 133 through 151 )
5X-RAY DIFFRACTION5chain 'A' and (resid 152 through 201 )
6X-RAY DIFFRACTION6chain 'A' and (resid 202 through 250 )
7X-RAY DIFFRACTION7chain 'A' and (resid 251 through 271 )

+
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