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- PDB-4bva: Crystal structure of the NADPH-T3 form of mouse Mu-crystallin. -

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Basic information

Entry
Database: PDB / ID: 4bva
TitleCrystal structure of the NADPH-T3 form of mouse Mu-crystallin.
ComponentsTHIOMORPHOLINE-CARBOXYLATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


thiomorpholine-carboxylate dehydrogenase / thiomorpholine-carboxylate dehydrogenase activity / Lysine catabolism / thyroid hormone metabolic process / thyroid hormone transport / hormone binding / mitochondrial transport / thyroid hormone binding / sensory perception of sound / transcription corepressor activity ...thiomorpholine-carboxylate dehydrogenase / thiomorpholine-carboxylate dehydrogenase activity / Lysine catabolism / thyroid hormone metabolic process / thyroid hormone transport / hormone binding / mitochondrial transport / thyroid 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 / cytoplasm
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 / 3,5,3'TRIIODOTHYRONINE / Ketimine reductase mu-crystallin
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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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)75,3238
Polymers72,4522
Non-polymers2,8716
Water9,692538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-33.3 kcal/mol
Surface area23090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.240, 97.140, 75.670
Angle α, β, γ (deg.)90.00, 104.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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
#2: 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
#3: Chemical ChemComp-T3 / 3,5,3'TRIIODOTHYRONINE / T3 / THYROID HORMONE / LIOTHYRONINE / Triiodothyronine


Mass: 650.973 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12I3NO4 / Comment: hormone*YM
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 538 / 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: 2.16 Å3/Da / Density % sol: 42.48 % / Description: NONE
Crystal growDetails: 200 MM KH2PO4, 15% PEG 3350, 280 MM NASCN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.75→42.7 Å / Num. obs: 63604 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.76 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.28
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 3.74 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.69 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2I99

2i99


Resolution: 1.75→42.68 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.801 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.19224 3181 5 %RANDOM
Rwork0.14624 ---
obs0.14857 60423 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.677 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å20.01 Å2
2---0.31 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.75→42.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4561 0 144 538 5243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194890
X-RAY DIFFRACTIONr_bond_other_d0.0010.024575
X-RAY DIFFRACTIONr_angle_refined_deg1.282.0086676
X-RAY DIFFRACTIONr_angle_other_deg0.734310541
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7645613
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48424.208183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.77115763
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4161525
X-RAY DIFFRACTIONr_chiral_restr0.0670.2768
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215464
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021045
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_it1.1851.4552449
X-RAY DIFFRACTIONr_mcbond_other1.1781.4542448
X-RAY DIFFRACTIONr_mcangle_it1.4772.1783063
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.67339465
X-RAY DIFFRACTIONr_sphericity_free21.8825180
X-RAY DIFFRACTIONr_sphericity_bonded6.02859719
LS refinement shellResolution: 1.748→1.794 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 232 -
Rwork0.188 4393 -
obs--97.88 %
Refinement TLS params.

T23: 0.0009 Å2 / 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)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.23620.0610.16160.10950.04060.1768-0.0031-0.0180.0109-0.0059-0.00060.0059-0.0169-0.01170.00370.02930.00580.00550.00310.008929.3110.128539.1387
20.02020.0468-0.00490.1150.02550.51260.00250.0032-0.0013-0.00850.0039-0.00410.0034-0.0258-0.00640.04090.0087-0.00710.00420.009217.8462-1.41342.1533
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 312
2X-RAY DIFFRACTION2B2 - 312

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