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- PDB-2bel: Structure of human 11-beta-hydroxysteroid dehydrogenase in comple... -

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Basic information

Entry
Database: PDB / ID: 2bel
TitleStructure of human 11-beta-hydroxysteroid dehydrogenase in complex with NADP and carbenoxolone
ComponentsCORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1
KeywordsOXIDOREDUCTASE / GLUCOCORTICOID ACTIVATION / DRUG TARGET / INHIBITOR / SHORT-CHAIN DEHYDROGENASE/REDUCTASE / HORMONE METABOLISM / MICROSOME / NADP / STEROID METABOLISM
Function / homology
Function and homology information


11beta-hydroxysteroid dehydrogenase / 11-beta-hydroxysteroid dehydrogenase (NADP+) activity / cortisol dehydrogenase activity / 7beta-hydroxysteroid dehydrogenase (NADP+) / 7-beta-hydroxysteroid dehydrogenase (NADP+) activity / Glucocorticoid biosynthesis / steroid catabolic process / Prednisone ADME / steroid binding / lung development ...11beta-hydroxysteroid dehydrogenase / 11-beta-hydroxysteroid dehydrogenase (NADP+) activity / cortisol dehydrogenase activity / 7beta-hydroxysteroid dehydrogenase (NADP+) / 7-beta-hydroxysteroid dehydrogenase (NADP+) activity / Glucocorticoid biosynthesis / steroid catabolic process / Prednisone ADME / steroid binding / lung development / NADP binding / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / protein homodimerization activity / membrane
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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
CARBENOXOLONE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 11-beta-hydroxysteroid dehydrogenase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsKavanagh, K. / Wu, X. / Svensson, S. / Elleby, B. / von Delft, F. / Debreczeni, J.E. / Sharma, S. / Bray, J. / Edwards, A. / Arrowsmith, C. ...Kavanagh, K. / Wu, X. / Svensson, S. / Elleby, B. / von Delft, F. / Debreczeni, J.E. / Sharma, S. / Bray, J. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Abrahmsen, L. / Oppermann, U.
CitationJournal: To be Published
Title: The High Resolution Structures of Human, Murine and Guinea Pig 11-Beta-Hydroxysteroid Dehydrogenase Type 1 Reveal Critical Differences in Active Site Architecture
Authors: Wu, X. / Kavanagh, K. / Svensson, S. / Elleby, B. / Hult, M. / von Delft, F. / Marsden, B. / Jornvall, H. / Abrahmsen, L. / Oppermann, U.
History
DepositionNov 25, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1
B: CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1
C: CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1
D: CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,82216
Polymers124,4244
Non-polymers5,39812
Water4,828268
1
A: CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1
B: CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9118
Polymers62,2122
Non-polymers2,6996
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1
D: CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9118
Polymers62,2122
Non-polymers2,6996
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)160.162, 112.984, 66.326
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.93801, 0.33752, 0.07885), (0.33814, 0.84112, 0.42212), (0.07615, 0.42261, -0.90311)-8.42495, 2.91119, -5.86785
2given(0.23114, 0.92361, 0.30582), (0.97182, -0.20419, -0.11782), (-0.04637, 0.32443, -0.94477)23.52363, 3.88708, -11.89135
3given(0.09458, 0.98932, 0.11088), (-0.99278, 0.08548, 0.08414), (0.07376, -0.11804, 0.99027)22.28565, -3.96804, -5.53188

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Components

#1: Protein
CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1 / HUMAN 11-BETA-HYDROXYSTEROID DEHYDROGENASE TYPE 1 / 11-DH / 11-BETA-HSD1


Mass: 31105.963 Da / Num. of mol.: 4 / Fragment: RESIDUES 26-284
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: P11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P28845, 11beta-hydroxysteroid 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-CBO / CARBENOXOLONE / Carbenoxolone


Mass: 570.757 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H50O7
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: CATALYZES REVERSIBLY THE CONVERSION OF CORTISOL TO THE INACTIVE METABOLITE CORTISONE.

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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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growpH: 5.5 / Details: 0.1 M MGCL2, 15% PEG 3350,, pH 5.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9765
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 2, 2004 / Details: MIRRORS
RadiationMonochromator: SI 1 1 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.1→61.08 Å / Num. obs: 68824 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.6
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.1 / % possible all: 84.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UNPUBLISHED MODEL OF HUMAN 11BETA HSD1

Resolution: 2.11→56.52 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.918 / SU B: 15.196 / SU ML: 0.184 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1953 2.8 %RANDOM
Rwork0.188 ---
obs0.19 66821 98 %-
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: 38.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å20 Å20 Å2
2--0.31 Å20 Å2
3----1.73 Å2
Refinement stepCycle: LAST / Resolution: 2.11→56.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7439 0 348 268 8055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227956
X-RAY DIFFRACTIONr_bond_other_d0.0010.027400
X-RAY DIFFRACTIONr_angle_refined_deg1.6072.01710870
X-RAY DIFFRACTIONr_angle_other_deg0.859317106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35751000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.65424.047257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.838151307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9981524
X-RAY DIFFRACTIONr_chiral_restr0.0930.21313
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028546
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021474
X-RAY DIFFRACTIONr_nbd_refined0.210.21724
X-RAY DIFFRACTIONr_nbd_other0.1690.27459
X-RAY DIFFRACTIONr_nbtor_refined0.180.23917
X-RAY DIFFRACTIONr_nbtor_other0.0870.24580
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2343
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0760.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2140.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0135158
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.96957932
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.67673237
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.138112936
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.11→2.16 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.306 115
Rwork0.288 4333
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)
12.3616-0.1717-0.21231.454-0.55382.37010.0328-0.3304-0.17050.3260.17430.2586-0.0543-0.2862-0.2071-0.12470.05230.09050.01570.14-0.0483-6.465118.362916.5308
21.4279-0.32710.68651.2343-0.5423.21230.08270.214-0.0542-0.0866-0.00550.0593-0.01380.1639-0.0772-0.220.04170.0147-0.04330.0271-0.13594.871123.527-12.8828
30.8367-0.6098-0.07023.6680.57431.00720.12680.21710.0961-1.1445-0.10360.0161-0.28050.0198-0.02320.2180.0159-0.0336-0.11650.0506-0.086544.6656-9.3341-20.5652
41.0576-0.5658-0.38273.04471.03012.0825-0.0422-0.1194-0.03610.21380.1087-0.16790.19340.1375-0.0665-0.17790.0026-0.0611-0.16860.0408-0.08642.3155.06067.7864
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 268
2X-RAY DIFFRACTION2B27 - 277
3X-RAY DIFFRACTION3C15 - 271
4X-RAY DIFFRACTION4D25 - 277

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