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- PDB-1y5m: The crystal structure of murine 11b-hydroxysteroid dehydrogenase:... -

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Basic information

Entry
Database: PDB / ID: 1y5m
TitleThe crystal structure of murine 11b-hydroxysteroid dehydrogenase: an important therapeutic target for diabetes
ComponentsCorticosteroid 11-beta-dehydrogenase, isozyme 1
KeywordsOXIDOREDUCTASE / ROSSMANN FOLD
Function / homology
Function and homology information


mineralocorticoid metabolic process / Glucocorticoid biosynthesis / glucocorticoid catabolic process / regulation of pentose-phosphate shunt / glucocorticoid biosynthetic process / 11beta-hydroxysteroid dehydrogenase / 11-beta-hydroxysteroid dehydrogenase (NADP+) activity / cortisol dehydrogenase activity / 7beta-hydroxysteroid dehydrogenase (NADP+) / 7-beta-hydroxysteroid dehydrogenase (NADP+) activity ...mineralocorticoid metabolic process / Glucocorticoid biosynthesis / glucocorticoid catabolic process / regulation of pentose-phosphate shunt / glucocorticoid biosynthetic process / 11beta-hydroxysteroid dehydrogenase / 11-beta-hydroxysteroid dehydrogenase (NADP+) activity / cortisol dehydrogenase activity / 7beta-hydroxysteroid dehydrogenase (NADP+) / 7-beta-hydroxysteroid dehydrogenase (NADP+) activity / Prednisone ADME / steroid catabolic process / steroid binding / lung development / apical part of cell / NADP binding / nuclear membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / protein homodimerization activity
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
Chem-NDP / N-OCTANE / 11-beta-hydroxysteroid dehydrogenase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.3 Å
AuthorsZhang, J. / Osslund, T.D. / Plant, M.H. / Clogston, C.L. / Nybo, R.E. / Xiong, F. / Delaney, J.M. / Jordan, S.R.
CitationJournal: Biochemistry / Year: 2005
Title: Crystal Structure of Murine 11-Hydroxysteroid Dehydrogenase 1: An Important Therapeutic Target for Diabetes
Authors: Zhang, J. / Osslund, T.D. / Plant, M.H. / Clogston, C.L. / Nybo, R.E. / Xiong, F. / Delaney, J.M. / Jordan, S.R.
History
DepositionDec 2, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Corticosteroid 11-beta-dehydrogenase, isozyme 1
B: Corticosteroid 11-beta-dehydrogenase, isozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,27510
Polymers61,1712
Non-polymers2,1048
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9550 Å2
ΔGint-98 kcal/mol
Surface area21080 Å2
MethodPISA
2
A: Corticosteroid 11-beta-dehydrogenase, isozyme 1
B: Corticosteroid 11-beta-dehydrogenase, isozyme 1
hetero molecules

A: Corticosteroid 11-beta-dehydrogenase, isozyme 1
B: Corticosteroid 11-beta-dehydrogenase, isozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,55020
Polymers122,3434
Non-polymers4,20716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/41
Buried area20810 Å2
ΔGint-219 kcal/mol
Surface area40440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.718, 96.718, 219.302
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Corticosteroid 11-beta-dehydrogenase, isozyme 1 / 11-DH / 11-beta-hydroxysteroid dehydrogenase 1 / 11-beta-HSD1 / 11beta-HSD1A


Mass: 30585.680 Da / Num. of mol.: 2 / Fragment: sequence database residues 24-292
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hsd11b1, Hsd11 / Plasmid: pAMG21 / Production host: Escherichia coli (E. coli) / Strain (production host): GM221
References: UniProt: P50172, 11beta-hydroxysteroid dehydrogenase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical ChemComp-OCT / N-OCTANE / Octane


Mass: 114.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.24 Å3/Da / Density % sol: 44.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 1.8 M Li2SO4, and 0.1 M Hepes buffer, pH 7.5 , VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 13, 2003 / Details: monochromator
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 47146 / Num. obs: 43963 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 17.5
Reflection shellResolution: 2.26→2.34 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.2 / % possible all: 91

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: SIRAS / Resolution: 2.3→40 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.25 3557 random
Rwork0.219 --
all-43963 -
obs-40406 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.583 Å20 Å20 Å2
2--4.583 Å20 Å2
3----9.165 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4078 0 218 126 4422
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.786
X-RAY DIFFRACTIONc_bond_d0.0828
X-RAY DIFFRACTIONc_mcbond_it1.3021.5
X-RAY DIFFRACTIONc_mcangle_it2.1152
X-RAY DIFFRACTIONc_scbond_it2.2922
X-RAY DIFFRACTIONc_scangle_it3.4272.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2N12.xprmdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4Octane.xprmion.top
X-RAY DIFFRACTION5SO4.xprm

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