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- PDB-4bv8: Crystal structure of the apo form of mouse Mu-crystallin. -

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Basic information

Entry
Database: PDB / ID: 4bv8
TitleCrystal structure of the apo 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
: / Ketimine reductase mu-crystallin
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,6235
Polymers72,4522
Non-polymers1703
Water3,729207
1
B: THIOMORPHOLINE-CARBOXYLATE DEHYDROGENASE
hetero molecules

A: THIOMORPHOLINE-CARBOXYLATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6235
Polymers72,4522
Non-polymers1703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
Buried area3320 Å2
ΔGint-25.2 kcal/mol
Surface area23460 Å2
MethodPISA
2
A: THIOMORPHOLINE-CARBOXYLATE DEHYDROGENASE
hetero molecules

B: THIOMORPHOLINE-CARBOXYLATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6235
Polymers72,4522
Non-polymers1703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
Buried area3320 Å2
ΔGint-25.2 kcal/mol
Surface area23460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.280, 96.550, 76.080
Angle α, β, γ (deg.)90.00, 103.28, 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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.47 Å3/Da / Density % sol: 49.8 % / Description: NONE
Crystal growpH: 8.5
Details: 10 MM TRIS-CL PH 8.5, 180 MM KH2PO4, 14.4% PEG 3350, 240 MM NASCN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→48.3 Å / Num. obs: 28087 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.4
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.52 / % possible all: 98.9

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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: 2.3→48.28 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 15.927 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24327 1404 5 %RANDOM
Rwork0.19241 ---
obs0.19495 26682 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.658 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20.37 Å2
2---0.6 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4435 0 8 207 4650
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194561
X-RAY DIFFRACTIONr_bond_other_d0.0010.024336
X-RAY DIFFRACTIONr_angle_refined_deg1.0971.9586219
X-RAY DIFFRACTIONr_angle_other_deg0.73339958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.475605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62524.061165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.77115695
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4981520
X-RAY DIFFRACTIONr_chiral_restr0.0590.2739
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215192
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02982
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_it0.9222.8192423
X-RAY DIFFRACTIONr_mcbond_other0.9212.8192422
X-RAY DIFFRACTIONr_mcangle_it1.6044.2223027
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.92.9292138
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 104 -
Rwork0.23 1988 -
obs--98.49 %
Refinement TLS params.

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)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.04860.0181-0.26420.1845-0.11791.89320.0218-0.0253-0.0117-0.03760.02370.00450.00310.0734-0.04550.0756-0.0134-0.02510.03570.02590.031717.9788-1.41831.8536
21.21240.23570.84390.25120.13840.643-0.03160.03930.04160.0052-0.00830.0215-0.03560.01460.03990.04220.00080.01030.01750.00620.05122.71239.9834-33.7865
30.21-0.05460.07510.0434-0.11130.46430.01080.0222-0.00150.0376-0.01160.0091-0.02520.01820.00080.1334-0.00330.00180.0063-0.01780.086511.10153.2796-15.2458
4189.7174149.68576.0662176.160461.180830.5217-3.97052.7661-1.2529-4.01444.3881-0.0908-1.63641.1517-0.41750.84130.156-0.09090.23780.0090.1077-9.0678-9.8524-40.7959
53.3665-5.09254.59267.7037-6.94716.26550.05730.0168-0.0278-0.0856-0.02190.04870.08160.0254-0.03540.09220.04310.02150.04710.06760.127918.93565.5013-19.0994
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 80
2X-RAY DIFFRACTION1A89 - 312
3X-RAY DIFFRACTION2B3 - 80
4X-RAY DIFFRACTION2B90 - 311
5X-RAY DIFFRACTION3A2001 - 2105
6X-RAY DIFFRACTION3B2001 - 2102
7X-RAY DIFFRACTION4B1312
8X-RAY DIFFRACTION5A1313
9X-RAY DIFFRACTION5B1313

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