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Basic information

Entry
Database: PDB / ID: 1xu7
TitleCrystal Structure of the Interface Open Conformation of Tetrameric 11b-HSD1
ComponentsCorticosteroid 11-beta-dehydrogenase, isozyme 1
KeywordsOXIDOREDUCTASE / 11b-HSD1 / SDR / dehydrogenase / hydroxysteroid
Function / homology
Function and homology information


cortisol dehydrogenase (NADP+) activity / 11-beta-hydroxysteroid dehydrogenase (NADP+) activity / 11beta-hydroxysteroid dehydrogenase / 7beta-hydroxysteroid dehydrogenase (NADP+) / 7-beta-hydroxysteroid dehydrogenase (NADP+) activity / Glucocorticoid biosynthesis / steroid catabolic process / Prednisone ADME / steroid binding / lung development ...cortisol dehydrogenase (NADP+) activity / 11-beta-hydroxysteroid dehydrogenase (NADP+) activity / 11beta-hydroxysteroid dehydrogenase / 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
Chem-NDP / 11-beta-hydroxysteroid dehydrogenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsHosfield, D.J. / Wu, Y. / Skene, R.J. / Hilger, M. / Jennings, A. / Snell, G.P. / Aertgeerts, K.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Conformational Flexibility in Crystal Structures of Human 11beta-hydroxysteroid dehydrogenase type I provide insights into glucocorticoid interconversion and enzyme regulation.
Authors: Hosfield, D.J. / Wu, Y. / Skene, R.J. / Hilger, M. / Jennings, A. / Snell, G.P. / Aertgeerts, K.
History
DepositionOct 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)134,01814
Polymers127,3484
Non-polymers6,67110
Water8,755486
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Corticosteroid 11-beta-dehydrogenase, isozyme 1
D: Corticosteroid 11-beta-dehydrogenase, isozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0097
Polymers63,6742
Non-polymers3,3355
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10290 Å2
ΔGint-63 kcal/mol
Surface area20330 Å2
MethodPISA, PQS
3
A: Corticosteroid 11-beta-dehydrogenase, isozyme 1
B: Corticosteroid 11-beta-dehydrogenase, isozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0097
Polymers63,6742
Non-polymers3,3355
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10110 Å2
ΔGint-61 kcal/mol
Surface area20710 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)56.430, 159.625, 73.544
Angle α, β, γ (deg.)90.00, 93.07, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological tetramer

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Components

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


Mass: 31836.875 Da / Num. of mol.: 4 / Mutation: C272S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSD11B1, HSD11, HSD11L / Plasmid: pBAD-ThioE / Cell (production host): DH10b-Tir / Production host: Escherichia coli (E. coli)
References: UniProt: P28845, 11beta-hydroxysteroid dehydrogenase
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.6 Å3/Da / Density % sol: 52.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG , MES buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1.3404, 1.3408, 1.3412, 1.2782
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.34041
21.34081
31.34121
41.27821
ReflectionResolution: 1.8→20 Å / Num. all: 114558 / Num. obs: 114558 / % possible obs: 95.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.046 / Net I/σ(I): 26.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 3 / Num. unique all: 9105 / Rsym value: 0.3 / % possible all: 76.2

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.488 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.128 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21716 5734 5 %RANDOM
Rwork0.19697 ---
all0.19796 108793 --
obs0.19796 108793 95.13 %-
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: 17.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å2-1.09 Å2
2---0.66 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8031 0 404 486 8921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0348605
X-RAY DIFFRACTIONr_angle_refined_deg1.2652.02111712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.05951044
X-RAY DIFFRACTIONr_chiral_restr0.0870.21409
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026040
X-RAY DIFFRACTIONr_nbd_refined0.1850.24822
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2667
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0750.218
X-RAY DIFFRACTIONr_mcbond_it0.3341.55192
X-RAY DIFFRACTIONr_mcangle_it0.66628351
X-RAY DIFFRACTIONr_scbond_it1.10433413
X-RAY DIFFRACTIONr_scangle_it1.8794.53361
LS refinement shellResolution: 1.8→1.843 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.289 324
Rwork0.25 6068

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