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- PDB-2fvl: Crystal structure of human 3-alpha hydroxysteroid/dihydrodiol deh... -

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Basic information

Entry
Database: PDB / ID: 2fvl
TitleCrystal structure of human 3-alpha hydroxysteroid/dihydrodiol dehydrogenase (AKR1C4) complexed with NADP+
ComponentsAldo-keto reductase family 1, member C4
KeywordsOXIDOREDUCTASE / Chlordecone reductase / aldo-keto reductase / 3alpha-HSD1 / DD4 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


chlordecone reductase / chlordecone reductase activity / C21-steroid hormone metabolic process / steroid dehydrogenase activity / bile acid transmembrane transporter activity / alcohol dehydrogenase (NADP+) activity / 3alpha-hydroxysteroid 3-dehydrogenase / cellular response to jasmonic acid stimulus / androsterone dehydrogenase activity / ketosteroid monooxygenase activity ...chlordecone reductase / chlordecone reductase activity / C21-steroid hormone metabolic process / steroid dehydrogenase activity / bile acid transmembrane transporter activity / alcohol dehydrogenase (NADP+) activity / 3alpha-hydroxysteroid 3-dehydrogenase / cellular response to jasmonic acid stimulus / androsterone dehydrogenase activity / ketosteroid monooxygenase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / progesterone metabolic process / aldo-keto reductase (NADPH) activity / bile acid biosynthetic process / bile acid and bile salt transport / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / daunorubicin metabolic process / doxorubicin metabolic process / bile acid binding / retinal dehydrogenase activity / aldose reductase (NADPH) activity / retinoid metabolic process / prostaglandin metabolic process / steroid metabolic process / androgen metabolic process / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Retinoid metabolism and transport / steroid binding / oxidoreductase activity / electron transfer activity / extracellular exosome / cytoplasm / cytosol
Similarity search - Function
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 ...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 / : / Aldo-keto reductase family 1 member C4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsUgochukwu, E. / Smee, C. / Guo, K. / Lukacik, P. / Kavanagh, K. / Debreczeni, J.E. / von Delft, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. ...Ugochukwu, E. / Smee, C. / Guo, K. / Lukacik, P. / Kavanagh, K. / Debreczeni, J.E. / von Delft, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human 3-alpha hydroxysteroid/dihydrodiol dehydrogenase (AKR1C4) complexed with NADP+
Authors: Ugochukwu, E. / Smee, C. / Guo, K. / Lukacik, P. / Kavanagh, K. / Debreczeni, J.E. / von Delft, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Oppermann, U.
History
DepositionJan 31, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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 C4
B: Aldo-keto reductase family 1, member C4
C: Aldo-keto reductase family 1, member C4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,1006
Polymers111,8703
Non-polymers2,2303
Water15,025834
1
A: Aldo-keto reductase family 1, member C4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0332
Polymers37,2901
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aldo-keto reductase family 1, member C4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0332
Polymers37,2901
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Aldo-keto reductase family 1, member C4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0332
Polymers37,2901
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.008, 166.008, 194.942
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41A
51B
61C
71A
81B
91C

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETSERSER5AA1 - 672 - 68
21METMETSERSER5BB1 - 672 - 68
31METMETSERSER5CC1 - 672 - 68
42LYSLYSVALVAL6AA68 - 7469 - 75
52LYSLYSVALVAL6BB68 - 7469 - 75
62LYSLYSVALVAL6CC68 - 7469 - 75
73LYSLYSTYRTYR5AA75 - 32376 - 324
83LYSLYSTYRTYR5BB75 - 32376 - 324
93LYSLYSTYRTYR5CC75 - 32376 - 324

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Components

#1: Protein Aldo-keto reductase family 1, member C4 / 3-alpha hydroxysteroid/dihydrodiol dehydrogenase


Mass: 37289.930 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1C4 / Plasmid: pNIC28-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: GenBank: 18088446, UniProt: P17516*PLUS, chlordecone reductase, 3alpha-hydroxysteroid 3-dehydrogenase (Si-specific)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 834 / 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: 5.999597 Å3/Da / Density % sol: 79.498619 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Potassium Citrate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Dec 23, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→196.12 Å / Num. obs: 104763 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.53 Å / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XF0.pdb

1xf0


Resolution: 2.4→32.73 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.982 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Some unexplained positive fofc density was found near to the following residues: - His117 A, B, C; - Lys247 A, B, C; - Arg301 A, B, C
RfactorNum. reflection% reflectionSelection details
Rfree0.20454 1972 1.9 %RANDOM
Rwork0.16648 ---
all0.1672 102788 --
obs0.1672 102788 98.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.205 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2---0.5 Å20 Å2
3---1 Å2
Refinement stepCycle: LAST / Resolution: 2.4→32.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7799 0 144 834 8777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228165
X-RAY DIFFRACTIONr_bond_other_d0.0010.025560
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.99811110
X-RAY DIFFRACTIONr_angle_other_deg0.9613.00213507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1675974
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40224.305374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.402151405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3071545
X-RAY DIFFRACTIONr_chiral_restr0.0860.21228
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028892
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021591
X-RAY DIFFRACTIONr_nbd_refined0.190.21460
X-RAY DIFFRACTIONr_nbd_other0.1880.25738
X-RAY DIFFRACTIONr_nbtor_refined0.1720.23868
X-RAY DIFFRACTIONr_nbtor_other0.0860.23922
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2609
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1250.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2140.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.244
X-RAY DIFFRACTIONr_mcbond_it4.37255407
X-RAY DIFFRACTIONr_mcbond_other1.42451921
X-RAY DIFFRACTIONr_mcangle_it4.68377915
X-RAY DIFFRACTIONr_scbond_it7.69893666
X-RAY DIFFRACTIONr_scangle_it8.761113191
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1854medium positional0.120.5
2B1854medium positional0.110.5
3C1854medium positional0.120.5
1A2515loose positional0.615
2B2515loose positional0.565
3C2515loose positional0.585
1A1854medium thermal0.832
2B1854medium thermal0.832
3C1854medium thermal0.812
1A2515loose thermal2.7810
2B2515loose thermal2.4810
3C2515loose thermal2.5610
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 114 -
Rwork0.257 6225 -
obs--81.47 %
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)
11.4462-0.305-0.33271.7388-0.1821.34370.00150.14950.0591-0.1909-0.00160.07510.07430.0620.0001-0.3267-0.0088-0.0289-0.34570.0701-0.358150.442964.647880.9397
21.5515-0.090.08582.8107-0.68261.37370.05010.32260.0447-0.36-0.07990.28970.0626-0.07750.0298-0.32150.0293-0.0407-0.20560.0123-0.218810.640442.317283.6506
31.38660.58780.56051.42050.61351.0282-0.04980.16970.0021-0.19320.0316-0.1186-0.14110.14180.0182-0.29830.0172-0.0007-0.3471-0.0897-0.281749.095119.738674.192
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 3232 - 324
2X-RAY DIFFRACTION2BB1 - 3232 - 324
3X-RAY DIFFRACTION3CC1 - 3232 - 324

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