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- PDB-4bv9: Crystal structure of the NADPH form of mouse Mu-crystallin. -

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Basic information

Entry
Database: PDB / ID: 4bv9
TitleCrystal structure of the NADPH form of mouse Mu-crystallin.
ComponentsTHIOMORPHOLINE-CARBOXYLATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Lysine catabolism / thiomorpholine-carboxylate dehydrogenase / thiomorpholine-carboxylate dehydrogenase activity / thyroid hormone metabolic process / thyroid hormone binding / thyroid hormone transport / hormone binding / sensory perception of sound / transcription corepressor activity / NADP binding ...Lysine catabolism / thiomorpholine-carboxylate dehydrogenase / thiomorpholine-carboxylate dehydrogenase activity / thyroid hormone metabolic process / thyroid hormone binding / thyroid hormone transport / hormone binding / sensory perception of sound / transcription corepressor activity / NADP binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / mitochondrion / nucleus / cytosol
Similarity search - Function
ornithine cyclodeaminase, domain 1 / ornithine cyclodeaminase, domain 1 / Ornithine cyclodeaminase/mu-crystallin / Ornithine cyclodeaminase, N-terminal / Ornithine cyclodeaminase/mu-crystallin family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / PYRUVIC ACID / Ketimine reductase mu-crystallin
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.193 Å
AuthorsBorel, F. / Hachi, I. / Palencia, A. / Gaillard, M.C. / Ferrer, J.L.
CitationJournal: FEBS J. / Year: 2014
Title: Crystal Structure of Mouse Mu-Crystallin Complexed with Nadph and the T3 Thyroid Hormone
Authors: Borel, F. / Hachi, I. / Palencia, A. / Gaillard, M.C. / Ferrer, J.L.
History
DepositionJun 25, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THIOMORPHOLINE-CARBOXYLATE DEHYDROGENASE
B: THIOMORPHOLINE-CARBOXYLATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3627
Polymers72,4522
Non-polymers1,9095
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-30.2 kcal/mol
Surface area22420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.840, 86.590, 93.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein THIOMORPHOLINE-CARBOXYLATE DEHYDROGENASE / MU-CRYSTALLIN HOMOLOG / NADP-REGULATED THYROID-HORMONE-BINDING PROTEIN / KETIMINE REDUCTASE


Mass: 36226.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PDEST / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2
References: UniProt: O54983, thiomorpholine-carboxylate dehydrogenase

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Non-polymers , 5 types, 241 molecules

#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 44.54 % / Description: NONE
Crystal growpH: 5.5
Details: 100 MM BIS TRIS PH 5.5, 23% PEG 3350, 100 MM AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 2, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.19→40.98 Å / Num. obs: 30724 / % possible obs: 95.4 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 21.28 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.96
Reflection shellResolution: 2.19→2.29 Å / Redundancy: 2.76 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.85 / % possible all: 91.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2I99

2i99


Resolution: 2.193→40.984 Å / SU ML: 0.22 / σ(F): 2 / Phase error: 25.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2614 1537 5 %
Rwork0.2129 --
obs0.2155 30716 95.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.7 Å2
Refinement stepCycle: LAST / Resolution: 2.193→40.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4524 0 123 236 4883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044744
X-RAY DIFFRACTIONf_angle_d0.8526470
X-RAY DIFFRACTIONf_dihedral_angle_d15.5431690
X-RAY DIFFRACTIONf_chiral_restr0.054759
X-RAY DIFFRACTIONf_plane_restr0.004816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1932-2.2640.32641330.27752523X-RAY DIFFRACTION93
2.264-2.34490.29111430.25492713X-RAY DIFFRACTION99
2.3449-2.43870.30121430.24982708X-RAY DIFFRACTION99
2.4387-2.54970.33991430.24312717X-RAY DIFFRACTION99
2.5497-2.68410.32141410.23572679X-RAY DIFFRACTION99
2.6841-2.85230.28971400.23592679X-RAY DIFFRACTION97
2.8523-3.07240.32221410.232667X-RAY DIFFRACTION97
3.0724-3.38150.28291380.21742623X-RAY DIFFRACTION95
3.3815-3.87040.22361390.18292643X-RAY DIFFRACTION94
3.8704-4.87510.18781360.1712583X-RAY DIFFRACTION92
4.8751-40.99090.21691400.18632644X-RAY DIFFRACTION90

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