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- PDB-2ipj: Crystal structure of h3alpha-hydroxysteroid dehydrogenase type 3 ... -

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Basic information

Entry
Database: PDB / ID: 2ipj
TitleCrystal structure of h3alpha-hydroxysteroid dehydrogenase type 3 mutant Y24A in complex with NADP+ and epi-testosterone
ComponentsAldo-keto reductase family 1 member C2
KeywordsOXIDOREDUCTASE / 3a-HSD / AKR1C21 / AKR / aldo-keto reductase / HSD / hydroxysteroid dehydrogenase / open conformation / epi-testosterone
Function / homology
Function and homology information


indanol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / 3(or 17)alpha-hydroxysteroid dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / indanol dehydrogenase activity / 3alpha-hydroxysteroid 3-dehydrogenase / phenanthrene 9,10-monooxygenase activity / cellular response to jasmonic acid stimulus / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity ...indanol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / 3(or 17)alpha-hydroxysteroid dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / indanol dehydrogenase activity / 3alpha-hydroxysteroid 3-dehydrogenase / phenanthrene 9,10-monooxygenase activity / cellular response to jasmonic acid stimulus / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity / androsterone dehydrogenase activity / cellular response to prostaglandin D stimulus / ketosteroid monooxygenase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / progesterone metabolic process / 17beta-estradiol 17-dehydrogenase / carboxylic acid binding / estradiol 17-beta-dehydrogenase [NAD(P)] activity / Oxidoreductases / daunorubicin metabolic process / doxorubicin metabolic process / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / bile acid binding / aldose reductase (NADPH) activity / prostaglandin metabolic process / steroid metabolic process / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / digestion / epithelial cell differentiation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / G protein-coupled receptor signaling pathway / positive regulation of cell population proliferation / cytosol
Similarity search - Function
Aldo-keto reductase family 1 member C / Aldo/keto reductase family putative active site signature. / 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 ...Aldo-keto reductase family 1 member C / Aldo/keto reductase family putative active site signature. / 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-FFA / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member C2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFaucher, F. / Cantin, L. / Pereira de Jesus-Tran, K. / Luu-the, V. / Labrie, F. / Breton, R.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Mouse 17alpha-Hydroxysteroid Dehydrogenase (AKR1C21) Binds Steroids Differently from other Aldo-keto Reductases: Identification and Characterization of Amino Acid Residues Critical for Substrate Binding.
Authors: Faucher, F. / Cantin, L. / Pereira de Jesus-Tran, K. / Lemieux, M. / Luu-The, V. / Labrie, F. / Breton, R.
History
DepositionOct 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3May 16, 2012Group: Other
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Aug 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldo-keto reductase family 1 member C2
B: Aldo-keto reductase family 1 member C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,91719
Polymers72,8962
Non-polymers3,02117
Water11,043613
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Aldo-keto reductase family 1 member C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9189
Polymers36,4481
Non-polymers1,4708
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
B: Aldo-keto reductase family 1 member C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,99810
Polymers36,4481
Non-polymers1,5509
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)144.788, 144.788, 203.885
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-325-

SO4

21A-418-

HOH

31B-416-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.8977, 0.4359, -0.0641), (0.4356, 0.8564, -0.2773), (-0.0659, -0.2769, -0.9586)202.1053, 12.0695, 397.9933

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Aldo-keto reductase family 1 member C2 / Trans-1 / 2- dihydrobenzene-1 / 2-diol dehydrogenase / Type III 3- alpha-hydroxysteroid ...Trans-1 / 2- dihydrobenzene-1 / 2-diol dehydrogenase / Type III 3- alpha-hydroxysteroid dehydrogenase / 3-alpha-HSD3 / Chlordecone reductase homolog HAKRD / Dihydrodiol dehydrogenase/bile acid-binding protein / DD/BABP / Dihydrodiol dehydrogenase 2 / DD2


Mass: 36447.891 Da / Num. of mol.: 2 / Mutation: Y24A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1C2 / Plasmid: pGEX1lT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLys
References: UniProt: P52895, Oxidoreductases, trans-1,2-dihydrobenzene-1,2-diol dehydrogenase, EC: 1.1.1.213

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Non-polymers , 6 types, 630 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-FFA / (10ALPHA,13ALPHA,14BETA,17ALPHA)-17-HYDROXYANDROST-4-EN-3-ONE / EPI-TESTOSTERONE / Epitestosterone


Mass: 288.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H28O2 / Comment: inhibitor, antagonist, hormone*YM
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 613 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.38 %
Crystal growTemperature: 277 K / Method: hanging drop / pH: 5.6
Details: PEG-4000 22%, 0.1M NaCitrate, pH 5.6, hanging drop, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Dec 3, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→19.98 Å / Num. all: 75962 / Num. obs: 75736 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 29.947 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.066 / Net I/σ(I): 18.29
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 4.4 / Num. measured obs: 82991 / Num. unique all: 11281 / Rsym value: 0.458 / % possible all: 97.6

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
CNS1.1refinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HDJ

2hdj


Resolution: 1.8→19.98 Å / Rfactor Rfree error: 0.004 / FOM work R set: 0.846 / Data cutoff high absF: 8881042 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.228 3811 5 %RANDOM
Rwork0.204 ---
obs-74951 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.737 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å21.49 Å20 Å2
2--1.65 Å20 Å2
3----3.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5132 0 193 613 5938
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_mcangle_it1.732
X-RAY DIFFRACTIONc_scbond_it1.692
X-RAY DIFFRACTIONc_scangle_it2.312.5
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
1.8-1.810.338770.31514271504
1.81-1.820.379640.30114581522
1.82-1.840.286650.28514351500
1.84-1.850.317800.29114051485
1.85-1.860.329900.29614341524
1.86-1.880.317820.28914291511
1.88-1.890.306790.28914141493
1.89-1.910.387680.34514351503
1.91-1.920.353780.35614611539
1.92-1.940.321830.32813821465
1.94-1.960.278750.25114441519
1.96-1.970.195680.23914201488
1.97-1.990.298610.23414521513
1.99-2.010.238760.24214201496
2.01-2.030.267890.23714461535
2.03-2.050.222680.23114521520
2.05-2.070.292670.26614431510
2.07-2.090.328580.30413931451
2.09-2.110.262690.22414821551
2.11-2.130.222740.21514171491
2.13-2.160.269800.21514621542
2.16-2.180.249770.22614201497
2.18-2.210.231680.21414211489
2.21-2.240.284900.22614421532
2.24-2.270.347850.27514001485
2.27-2.30.259840.22814381522
2.3-2.330.274680.22414471515
2.33-2.370.265670.22314341501
2.37-2.40.27810.22114481529
2.4-2.440.243820.21614411523
2.44-2.490.233850.20814101495
2.49-2.530.195700.19414471517
2.53-2.580.24880.20914501538
2.58-2.630.267700.20714561526
2.63-2.690.209740.19314391513
2.69-2.750.219850.19614291514
2.75-2.820.207830.19314301513
2.82-2.90.239720.20314561528
2.9-2.980.215760.19914261502
2.98-3.080.182790.18214741553
3.08-3.190.23680.19414351503
3.19-3.320.212750.18714431518
3.32-3.470.226880.18914771565
3.47-3.650.175860.17914091495
3.65-3.880.175660.15914761542
3.88-4.180.189700.15714811551
4.18-4.60.169770.14614531530
4.6-5.260.158840.14214701554
5.26-6.630.239740.18915061580
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ligands_.paramligands_.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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