[English] 日本語
Yorodumi
- PDB-3qwi: Crystal structure of a 17beta-hydroxysteroid dehydrogenase (holo ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qwi
TitleCrystal structure of a 17beta-hydroxysteroid dehydrogenase (holo form) from fungus Cochliobolus lunatus in complex with NADPH and coumestrol
Components17beta-hydroxysteroid dehydrogenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / 17BETA-HYDROXYSTEROID DEHYDROGENASE / SHORT CHAIN DEHYDROGENASE/REDUCTASE / PHYTOESTROGENS / FLAVONOID / 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
Coumestrol / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 17beta-hydroxysteroid dehydrogenase
Similarity search - Component
Biological speciesCochliobolus lunatus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCassetta, A. / Lamba, D. / Krastanova, I. / Stojan, J. / Lanisnik Rizner, T. / Kristan, K. / Brunskole, M.
CitationJournal: Biochem.J. / Year: 2012
Title: Structural studies on the flavonoid inhibition of a fungal 17Beta-Hydroxysteroid dehydrogenase
Authors: Cassetta, A. / Krastanova, I. / Kristan, K. / Brunskole Svegelj, M. / Lamba, D. / Lanisnik Rizner, T. / Stojan, J.
History
DepositionFeb 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Non-polymer description
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)120,08320
Polymers115,7464
Non-polymers4,33716
Water5,927329
1
A: 17beta-hydroxysteroid dehydrogenase
B: 17beta-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,14510
Polymers57,8732
Non-polymers2,2728
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-20 kcal/mol
Surface area20050 Å2
MethodPISA
2
C: 17beta-hydroxysteroid dehydrogenase
D: 17beta-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,93810
Polymers57,8732
Non-polymers2,0658
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-16 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.410, 116.810, 70.430
Angle α, β, γ (deg.)90.00, 103.14, 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-CUE / Coumestrol / 3,9-dihydroxy-6H-[1]benzofuro[3,2-c]chromen-6-one / Coumestrol


Mass: 268.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H8O5
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.19 Å3/Da / Density % sol: 43.95 %
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 COUMESTROL, PH 7.9, VAPOR DIFFUSION, ...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 COUMESTROL, 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: 2.5→34.29 Å / Num. all: 34093 / Num. obs: 34093 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 40.3 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 11.3
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 3 / Num. unique all: 12947 / Rsym value: 0.347 / % possible all: 91.6

-
Processing

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

3qwf


Resolution: 2.5→33.86 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.895 / SU B: 20.507 / SU ML: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23264 1710 5 %RANDOM
Rwork0.16104 ---
all0.1646 34071 --
obs0.1646 34071 98 %-
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: 30.013 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.01 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refine analyzeLuzzati coordinate error obs: 0.278 Å
Refinement stepCycle: LAST / Resolution: 2.5→33.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7858 0 288 329 8475
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0228317
X-RAY DIFFRACTIONr_angle_refined_deg1.1111.97711293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.43551037
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85923.689347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.548151293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4831548
X-RAY DIFFRACTIONr_chiral_restr0.0770.21259
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216251
X-RAY DIFFRACTIONr_mcbond_it0.2861.55125
X-RAY DIFFRACTIONr_mcangle_it0.55928210
X-RAY DIFFRACTIONr_scbond_it0.9233192
X-RAY DIFFRACTIONr_scangle_it1.5654.53083
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 92 -
Rwork0.253 2121 -
obs-2213 86.92 %
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)
11.18650.31320.20351.1179-0.41071.5246-0.0255-0.0107-0.24950.0334-0.05790.0290.11710.04360.08340.0374-0.00080.01990.0127-0.00020.0862-13.041-17.007920.1972
21.33410.4465-0.08651.3311-0.41551.293-0.00460.10340.1128-0.10430.01270.0944-0.0664-0.1164-0.00810.0462-0.0061-0.02380.04660.01080.0247-14.55634.0641-3.403
31.45220.22970.12841.0879-0.34651.3688-0.0325-0.14020.0970.20920.0025-0.0177-0.0987-0.03980.03010.0548-0.0063-0.0150.0478-0.00770.01456.40933.079233.5347
41.10410.14340.1321.2878-0.26091.48170.01170.12520.0676-0.1201-0.0603-0.24540.05880.13540.04870.0244-0.0070.02030.0590.03090.071215.01349.73363.6204
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 270
2X-RAY DIFFRACTION1A271
3X-RAY DIFFRACTION1A272
4X-RAY DIFFRACTION2B12 - 270
5X-RAY DIFFRACTION2B271
6X-RAY DIFFRACTION3C10 - 270
7X-RAY DIFFRACTION3C271
8X-RAY DIFFRACTION3C273
9X-RAY DIFFRACTION4D10 - 270
10X-RAY DIFFRACTION4D271
11X-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