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- PDB-1q13: Crystal structure of rabbit 20alpha hyroxysteroid dehydrogenase i... -

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Basic information

Entry
Database: PDB / ID: 1q13
TitleCrystal structure of rabbit 20alpha hyroxysteroid dehydrogenase in ternary complex with NADP and testosterone
ComponentsProstaglandin-E2 9-reductase
KeywordsOXIDOREDUCTASE / 20alpha-HSD / hydroxysteroid dehydrogenase / aldo-keto reductase / TIM-barrel / AKR / testosterone / ternary complex
Function / homology
Function and homology information


prostaglandin-E2 9-reductase / prostaglandin E2 9-reductase activity / 20alpha-hydroxysteroid dehydrogenase / 17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase [NAD(P)+] activity / prostaglandin biosynthetic process / cytoplasm
Similarity search - Function
Aldo-keto reductase family 1 member C / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / 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 ...Aldo-keto reductase family 1 member C / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / TESTOSTERONE / Prostaglandin-E(2) 9-reductase
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsCouture, J.-F. / Cantin, L. / Legrand, P. / Luu-The, V. / Labrie, F. / Breton, R.
CitationJournal: J. Mol. Biol. / Year: 2004
Title: Loop relaxation, a mechanism that explains the reduced specificity of rabbit 20alpha-hydroxysteroid dehydrogenase, a member of the aldo-keto reductase superfamily.
Authors: Couture, J.F. / Legrand, P. / Cantin, L. / Labrie, F. / Luu-The, V. / Breton, R.
History
DepositionJul 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.5Feb 14, 2024Group: 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 / 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_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prostaglandin-E2 9-reductase
B: Prostaglandin-E2 9-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3126
Polymers73,4402
Non-polymers1,8714
Water7,062392
1
A: Prostaglandin-E2 9-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8484
Polymers36,7201
Non-polymers1,1283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Prostaglandin-E2 9-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4642
Polymers36,7201
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.210, 84.046, 66.249
Angle α, β, γ (deg.)90.00, 91.17, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
171A
181B
191A
201B
211A
221B
231A
241B
251A
261B
271A
281B
291A
301B
311A
321B
331A
341B
12A
22B

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSARGARGAA4 - 74 - 7
211LYSLYSARGARGBB4 - 74 - 7
321ASPASPTYRTYRAA12 - 2412 - 24
421ASPASPTYRTYRBB12 - 2412 - 24
531ILEILEILEILEAA40 - 4240 - 42
631ILEILEILEILEBB40 - 4240 - 42
741ALAALAHISHISAA44 - 4844 - 48
841ALAALAHISHISBB44 - 4844 - 48
951ASPASPGLUGLUAA50 - 5850 - 58
1051ASPASPGLUGLUBB50 - 5850 - 58
1161ASPASPPROPROAA78 - 9278 - 92
1261ASPASPPROPROBB78 - 9278 - 92
1371PROPROLEULEUAA97 - 9997 - 99
1471PROPROLEULEUBB97 - 9997 - 99
1581VALVALALAALAAA111 - 121111 - 121
1681VALVALALAALABB111 - 121111 - 121
1791ILEILETRPTRPAA144 - 148144 - 148
1891ILEILETRPTRPBB144 - 148144 - 148
19101ALAALAGLUGLUAA150 - 152150 - 152
20101ALAALAGLUGLUBB150 - 152150 - 152
21111CYSCYSARGARGAA154 - 170154 - 170
22111CYSCYSARGARGBB154 - 170154 - 170
23121PROPROGLNGLNAA186 - 199186 - 199
24121PROPROGLNGLNBB186 - 199186 - 199
25131LEULEUGLUGLUAA202 - 224202 - 224
26131LEULEUGLUGLUBB202 - 224202 - 224
27141PROPROVALVALAA225 - 234225 - 234
28141PROPROVALVALBB225 - 234225 - 234
29151GLNGLNSERSERAA250 - 271250 - 271
30151GLNGLNSERSERBB250 - 271250 - 271
31161VALVALSERSERAA295 - 298295 - 298
32161VALVALSERSERBB295 - 298295 - 298
33171PROPROASPASPAA318 - 321318 - 321
34171PROPROASPASPBB318 - 321318 - 321
112NAPNAPNAPNAPAD401
212NAPNAPNAPNAPBF402

NCS ensembles :
ID
1
2

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Components

#1: Protein Prostaglandin-E2 9-reductase / 20-alpha-hydroxysteroid dehydrogenase / 20-alpha-HSD


Mass: 36720.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): Bl-21(DE3)pLysS
References: UniProt: P80508, prostaglandin-E2 9-reductase, 20alpha-hydroxysteroid dehydrogenase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-TES / TESTOSTERONE


Mass: 288.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28O2 / Comment: hormone*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.17 Å3/Da / Density % sol: 43.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG4000, ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 7, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.08→5.06 Å / Num. all: 81288 / Num. obs: 37115 / Observed criterion σ(F): 7.2 / Observed criterion σ(I): 13
Reflection shellResolution: 2.1→2.15 Å / % possible all: 59

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→20 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.86 / SU B: 8.783 / SU ML: 0.228 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2.1 / ESU R: 0.354 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28008 1754 5 %RANDOM
Rwork0.22643 ---
obs0.22918 33320 93.54 %-
all-76308 --
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: 15.287 Å2
Baniso -1Baniso -2Baniso -3
1--5.09 Å20 Å20.16 Å2
2--0.06 Å20 Å2
3---5.04 Å2
Refinement stepCycle: LAST / Resolution: 2.08→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5111 0 122 392 5625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0225366
X-RAY DIFFRACTIONr_angle_refined_deg2.0131.9927286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1775636
X-RAY DIFFRACTIONr_chiral_restr0.1340.2798
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024006
X-RAY DIFFRACTIONr_nbd_refined0.2950.23156
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2650.2450
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5610.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4770.216
X-RAY DIFFRACTIONr_mcbond_it0.9151.53198
X-RAY DIFFRACTIONr_mcangle_it1.38825178
X-RAY DIFFRACTIONr_scbond_it2.42332168
X-RAY DIFFRACTIONr_scangle_it3.4274.52108
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1268tight positional0.090.05
22B48tight positional0.090.05
11A1268tight thermal0.250.3
22B48tight thermal0.480.3
LS refinement shellResolution: 2.084→2.175 Å / Total num. of bins used: 12 /
RfactorNum. reflection
Rfree0.307 188
Rwork0.258 3649
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)
10.88250.4683-0.08421.3726-0.24041.3053-0.01190.03810.07240.03310.01680.0702-0.06150.0929-0.00490.78050.0082-0.00040.29140.01650.015915.9940.38832.043
20.72180.3047-0.14261.0060.21021.0648-0.04510.0049-0.0203-0.0014-0.0144-0.010.0062-0.14020.05950.7925-0.0024-0.01010.3584-0.01180.047541.6810.819-0.28
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 3232 - 323
2X-RAY DIFFRACTION1AD4011
3X-RAY DIFFRACTION1AF5011
4X-RAY DIFFRACTION1AG602 - 8021 - 201
5X-RAY DIFFRACTION2BB2 - 3232 - 323
6X-RAY DIFFRACTION2BE4021
7X-RAY DIFFRACTION2BH405 - 5933 - 191

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