[English] 日本語
Yorodumi
- PDB-4fj0: Crystal structure of the ternary complex between a fungal 17beta-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fj0
TitleCrystal structure of the ternary complex between a fungal 17beta-hydroxysteroid dehydrogenase (Holo form) and 3,7-dihydroxy flavone
Components17beta-hydroxysteroid dehydrogenase
Keywordsoxidoreductase/Oxidoreductase inhibitor / Short chain Dehydrogenase/Reductase / Rossmann Fold / Oxidoreductase / NADP(H) / oxidoreductase-Oxidoreductase inhibitor complex
Function / homology
Function and homology information


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
3,7-dihydroxy-2-phenyl-4H-chromen-4-one / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 17beta-hydroxysteroid dehydrogenase
Similarity search - Component
Biological speciesCochliobolus lunatus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCassetta, A. / Lamba, D. / Krastanova, I.
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
DepositionJun 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Structure summary
Revision 1.2Jul 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 1.3Sep 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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)119,72518
Polymers115,7464
Non-polymers3,97914
Water4,864270
1
A: 17beta-hydroxysteroid dehydrogenase
B: 17beta-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8629
Polymers57,8732
Non-polymers1,9897
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-14 kcal/mol
Surface area19800 Å2
MethodPISA
2
C: 17beta-hydroxysteroid dehydrogenase
D: 17beta-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8629
Polymers57,8732
Non-polymers1,9897
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-19 kcal/mol
Surface area19460 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21240 Å2
ΔGint-72 kcal/mol
Surface area32160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.340, 113.250, 69.310
Angle α, β, γ (deg.)90.00, 102.76, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRAA11 - 27011 - 270
21TYRTYRBB11 - 27011 - 270
12ILEILEAA12 - 26912 - 269
22ILEILECC12 - 26912 - 269
13TYRTYRAA11 - 26911 - 269
23TYRTYRDD11 - 26911 - 269
14ILEILEBB12 - 26912 - 269
24ILEILECC12 - 26912 - 269
15TYRTYRBB11 - 26911 - 269
25TYRTYRDD11 - 26911 - 269
16ILEILECC12 - 26912 - 269
26ILEILEDD12 - 26912 - 269

NCS ensembles :
ID
1
2
3
4
5
6
DetailsTwo functionally active dimers are present in the asymmetric unit: Dimer 1: chains A:B Dimer 2: chains C:D

-
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): BL21
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-HHF / 3,7-dihydroxy-2-phenyl-4H-chromen-4-one


Mass: 254.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.06 Å3/Da / Density % sol: 40.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% (W/V) PEG 2000 MME, 0.1M KCNS, 5 mM NADP. Crystals soaked for 24 hours in: 30% (W/V) PEG 2000 MME, 0.1M KCNS, 15% (V/V)ETHYLENE GLYCOLE, 5% (V/V) DMSO, 1 mM NADP, 0.8 mM 3,7- ...Details: 30% (W/V) PEG 2000 MME, 0.1M KCNS, 5 mM NADP. Crystals soaked for 24 hours in: 30% (W/V) PEG 2000 MME, 0.1M KCNS, 15% (V/V)ETHYLENE GLYCOLE, 5% (V/V) DMSO, 1 mM NADP, 0.8 mM 3,7-dihydroxyflavone, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 16, 2010 / Details: Platinum coated cylindrical mirror
RadiationMonochromator: Si (1 1 1) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.2→45 Å / Num. all: 45372 / Num. obs: 45372 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 11.8
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 2.65 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 3.71 / Num. unique all: 6010 / % possible all: 82.4

-
Processing

Software
NameVersionClassification
XRD1beamline softwaredata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QWI

3qwi


Resolution: 2.2→43.41 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 11.991 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.362 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20469 2269 5 %RANDOM
Rwork0.16997 ---
all0.17173 43102 --
obs0.17173 43102 95.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.731 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å2-1.71 Å2
2--1.25 Å20 Å2
3----1.34 Å2
Refine analyzeLuzzati coordinate error obs: 0.249 Å
Refinement stepCycle: LAST / Resolution: 2.2→43.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7851 0 262 270 8383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.028280
X-RAY DIFFRACTIONr_bond_other_d0.0050.025439
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.97311236
X-RAY DIFFRACTIONr_angle_other_deg1.2083.00213106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.68951036
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.95223.689347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.676151292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.8521548
X-RAY DIFFRACTIONr_chiral_restr0.0810.21257
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029244
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021672
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A89410.08
12B89410.08
21A89170.07
22C89170.07
31A89210.08
32D89210.08
41B88660.09
42C88660.09
51B89340.08
52D89340.08
61C87880.09
62D87880.09
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 134 -
Rwork0.207 2558 -
obs-2558 76.83 %
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)
11.1188-0.06270.22831.0531-0.35621.8374-0.0187-0.1186-0.1434-0.00580.0580.01640.1698-0.0458-0.03930.0413-0.01770.00810.03030.01310.0766-13.2958-16.174921.0936
21.44940.1594-0.09591.1837-0.4131.305-0.01660.03790.123-0.10010.03630.1138-0.0555-0.1117-0.01970.037-0.0003-0.03640.0316-0.00180.0544-14.14364.4052-2.7344
31.15650.4132-0.27891.394-0.41751.71960.0112-0.19680.09680.1525-0.00360.0912-0.0804-0.0743-0.00760.02090.01070.00410.0637-0.02740.01986.6783.095533.5833
40.7889-0.0020.25011.0491-0.27161.56630.02240.06180.0046-0.1395-0.0357-0.1290.05240.12960.01340.028-0.00170.01410.02380.00520.049315.10229.42994.0015
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 270
2X-RAY DIFFRACTION1A302
3X-RAY DIFFRACTION1A303
4X-RAY DIFFRACTION2B11 - 270
5X-RAY DIFFRACTION2B302
6X-RAY DIFFRACTION2B303
7X-RAY DIFFRACTION2B304
8X-RAY DIFFRACTION3C12 - 270
9X-RAY DIFFRACTION3C302
10X-RAY DIFFRACTION3C303
11X-RAY DIFFRACTION4D10 - 270
12X-RAY DIFFRACTION4D303

+
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