[English] 日本語
Yorodumi
- PDB-3qwh: Crystal structure of the 17beta-hydroxysteroid dehydrogenase from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qwh
TitleCrystal structure of the 17beta-hydroxysteroid dehydrogenase from Cochliobolus lunatus in complex with NADPH and kaempferol
Components17beta-hydroxysteroid dehydrogenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / 17BETA-HYDROXYSTEROID DEHYDROGENASE / SHORT CHAIN DEHYDROGENASE/REDUCTASE / PHYTOESTROGENS / FLAVONOIDS / Rossmann Fold / Cytosol / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


organic substance biosynthetic process / cellular biosynthetic process / oxidoreductase activity, acting on CH-OH group of donors / nucleotide binding
Similarity search - Function
PKS_KR / 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
Chem-KMP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / DI(HYDROXYETHYL)ETHER / 17beta-hydroxysteroid dehydrogenase
Similarity search - Component
Biological speciesCochliobolus lunatus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsCassetta, A. / Lamba, D. / Krastanova, I. / Stojan, J. / Rizner, T.L. / Kristan, K. / Brunskole, M.
CitationJournal: J. Steroid Biochem. Mol. Biol. / Year: 2017
Title: Structural basis for inhibition of 17 beta-hydroxysteroid dehydrogenases by phytoestrogens: The case of fungal 17 beta-HSDcl.
Authors: Cassetta, A. / Stojan, J. / Krastanova, I. / Kristan, K. / Brunskole Svegelj, M. / Lamba, D. / Rizner, T.L.
History
DepositionFeb 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.name
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 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: 17beta-hydroxysteroid dehydrogenase
B: 17beta-hydroxysteroid dehydrogenase
C: 17beta-hydroxysteroid dehydrogenase
D: 17beta-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,68512
Polymers115,7464
Non-polymers3,9388
Water4,197233
1
A: 17beta-hydroxysteroid dehydrogenase
B: 17beta-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0387
Polymers57,8732
Non-polymers2,1655
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-39 kcal/mol
Surface area19730 Å2
MethodPISA
2
C: 17beta-hydroxysteroid dehydrogenase
D: 17beta-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6465
Polymers57,8732
Non-polymers1,7733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-34 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.950, 116.640, 70.240
Angle α, β, γ (deg.)90.00, 102.54, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
17beta-hydroxysteroid dehydrogenase


Mass: 28936.545 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cochliobolus lunatus (fungus) / Strain: M118 / Gene: 17HSDcl / Plasmid: PGEX / Production host: Escherichia coli (E. coli) / Strain (production host): JM107
References: UniProt: O93874, 17beta-estradiol 17-dehydrogenase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-KMP / 3,5,7-TRIHYDROXY-2-(4-HYDROXYPHENYL)-4H-CHROMEN-4-ONE / KAEMPHEROL / Kaempferol


Mass: 286.236 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H10O6
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.17 Å3/Da / Density % sol: 43.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 30% (W/V) PEG 2000 MME, 0.1M KCNS, 15% (V/V) Crystals soaked in: 30% (W/V) PEG 2000 MME, 0.1M KCNS, 15% (V/V)ETHYLENE GLYCOLE, 5% (V/V) DMSO, 2MM KAEMPFEROL, PH 7.9, VAPOR DIFFUSION, HANGING ...Details: 30% (W/V) PEG 2000 MME, 0.1M KCNS, 15% (V/V) Crystals soaked in: 30% (W/V) PEG 2000 MME, 0.1M KCNS, 15% (V/V)ETHYLENE GLYCOLE, 5% (V/V) DMSO, 2MM KAEMPFEROL, PH 7.9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 5, 2008 / Details: PT-COATED TOROIDAL MIRROR
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.61→39.1 Å / Num. all: 28133 / Num. obs: 28133 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 46 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 12.5
Reflection shellResolution: 2.61→2.75 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 5 / Num. unique all: 3279 / Rsym value: 0.187 / % possible all: 75.5

-
Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.5.0094refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QWF

3qwf


Resolution: 2.62→39.1 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.897 / SU B: 28.239 / SU ML: 0.263 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1410 5 %RANDOM
Rwork0.168 ---
all0.17188 28102 --
obs0.17188 28102 94.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.801 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.316 Å
Refinement stepCycle: LAST / Resolution: 2.62→39.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7843 0 262 233 8338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228280
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.97611254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.65151035
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.25323.689347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.868151291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5921548
X-RAY DIFFRACTIONr_chiral_restr0.0840.21256
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216242
X-RAY DIFFRACTIONr_mcbond_it0.321.55114
X-RAY DIFFRACTIONr_mcangle_it0.62528190
X-RAY DIFFRACTIONr_scbond_it133166
X-RAY DIFFRACTIONr_scangle_it1.6644.53064
LS refinement shellResolution: 2.617→2.684 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 79 -
Rwork0.3 1290 -
obs-1290 63.12 %
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)
11.15830.21030.23961.0281-0.47671.2104-0.0303-0.0068-0.26010.0668-0.02410.00480.1240.00020.05440.0404-0.00820.0191-0.0044-0.00260.0567-12.7714-16.973220.2167
21.3020.43630.18331.1438-0.64590.9450.01350.11060.149-0.0465-0.01860.1234-0.0595-0.12860.00510.0151-0.0013-0.00860.0510.01770.0149-14.66154.127-3.1709
30.94620.5084-0.07421.0667-0.33871.3273-0.0208-0.12060.12480.2009-0.0276-0.0333-0.0943-0.05660.04840.04420-0.01270.0441-0.01290.00876.65413.267933.4174
40.86770.01840.07121.3039-0.33691.5305-0.01580.14830.0211-0.1502-0.0197-0.31220.09270.13030.03550.0143-0.00810.03130.03590.01590.088115.00799.83653.5
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 270
2X-RAY DIFFRACTION1A272
3X-RAY DIFFRACTION2B14 - 270
4X-RAY DIFFRACTION2B272
5X-RAY DIFFRACTION3C14 - 270
6X-RAY DIFFRACTION4D10 - 270
7X-RAY DIFFRACTION4D272

+
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