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- PDB-6nj7: 11-BETA DEHYDROGENASE ISOZYME 1 IN COMPLEX WITH COLLETOIC ACID -

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Basic information

Entry
Database: PDB / ID: 6nj7
Title11-BETA DEHYDROGENASE ISOZYME 1 IN COMPLEX WITH COLLETOIC ACID
ComponentsCorticosteroid 11-beta-dehydrogenase isozyme 1
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / INHIBITOR / COMPLEX / GLUCOCORTICOID REGULATION
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-7H6 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 11-beta-hydroxysteroid dehydrogenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMiller, D.J. / Rivas, F.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Mechanistic Insight on the Mode of Action of Colletoic Acid.
Authors: Ling, T. / Miller, D.J. / Lang, W.H. / Griffith, E. / Rodriguez-Cortes, A. / El Ayachi, I. / Palacios, G. / Min, J. / Miranda-Carboni, G. / Lee, R.E. / Rivas, F.
History
DepositionJan 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)132,68412
Polymers128,7014
Non-polymers3,9838
Water724
1
A: Corticosteroid 11-beta-dehydrogenase isozyme 1
B: Corticosteroid 11-beta-dehydrogenase isozyme 1
hetero molecules

C: Corticosteroid 11-beta-dehydrogenase isozyme 1
D: Corticosteroid 11-beta-dehydrogenase isozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,68412
Polymers128,7014
Non-polymers3,9838
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Buried area14270 Å2
ΔGint-99 kcal/mol
Surface area36720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.022, 153.749, 74.051
Angle α, β, γ (deg.)90.00, 93.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Corticosteroid 11-beta-dehydrogenase isozyme 1 / 11-beta-hydroxysteroid dehydrogenase 1 / 11-beta-HSD1 / Short chain dehydrogenase/reductase family ...11-beta-hydroxysteroid dehydrogenase 1 / 11-beta-HSD1 / Short chain dehydrogenase/reductase family 26C member 1


Mass: 32175.279 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSD11B1, HSD11, HSD11L, SDR26C1
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: P28845, 11beta-hydroxysteroid dehydrogenase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-7H6 / (1S,4S,5S,9S)-9-hydroxy-8-methyl-4-(propan-2-yl)spiro[4.5]dec-7-ene-1-carboxylic acid


Mass: 252.349 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H24O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: THE 4 UL DROP CONTAINED 2 UL PROTEIN (25 MM TRIS, PH 8.0, 250 MM NACL, 4 MM CHAPS, 10 MG/ML PROTEIN) AND 2 UL WELL SOLUTION (100 MM MES, PH 6.5, 20 PEG 4000), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→76.87 Å / Num. obs: 38505 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rsym value: 0.038 / Net I/σ(I): 2
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.1 % / Rsym value: 0.613 / % possible all: 89.9

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0123refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D5Q

3d5q


Resolution: 2.6→76.87 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 17.24 / SU ML: 0.334 / Cross valid method: THROUGHOUT / ESU R: 0.583 / ESU R Free: 0.315 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1930 5 %RANDOM
Rwork0.213 ---
obs0.215 36549 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 93.48 Å2
Baniso -1Baniso -2Baniso -3
1-6.74 Å20 Å2-3.11 Å2
2---2.77 Å20 Å2
3----3.59 Å2
Refinement stepCycle: LAST / Resolution: 2.6→76.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7128 0 264 4 7396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197512
X-RAY DIFFRACTIONr_bond_other_d0.0020.026990
X-RAY DIFFRACTIONr_angle_refined_deg1.3562.00110253
X-RAY DIFFRACTIONr_angle_other_deg0.938315946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6715990
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22923.992238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.863151113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1721527
X-RAY DIFFRACTIONr_chiral_restr0.0610.21262
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028450
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021627
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.2659.6843984
X-RAY DIFFRACTIONr_mcbond_other5.2659.6833983
X-RAY DIFFRACTIONr_mcangle_it7.75514.5224966
X-RAY DIFFRACTIONr_mcangle_other7.75514.5244967
X-RAY DIFFRACTIONr_scbond_it6.69610.0373528
X-RAY DIFFRACTIONr_scbond_other6.69510.0373529
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.82214.8615288
X-RAY DIFFRACTIONr_long_range_B_refined11.59477.5228243
X-RAY DIFFRACTIONr_long_range_B_other11.59477.5268244
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 110 -
Rwork0.36 2418 -
obs--88.24 %

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