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- PDB-1upl: Crystal structure of MO25 alpha -

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Basic information

Entry
Database: PDB / ID: 1upl
TitleCrystal structure of MO25 alpha
ComponentsMO25 PROTEIN
KeywordsTRANSFERASE / STRAD / LKB1 / ARMADILLO
Function / homology
Function and homology information


regulation of transmembrane transport / cellular hypotonic response / Energy dependent regulation of mTOR by LKB1-AMPK / serine/threonine protein kinase complex / protein kinase activator activity / signaling adaptor activity / protein serine/threonine kinase activator activity / protein serine/threonine kinase binding / kinase binding / secretory granule lumen ...regulation of transmembrane transport / cellular hypotonic response / Energy dependent regulation of mTOR by LKB1-AMPK / serine/threonine protein kinase complex / protein kinase activator activity / signaling adaptor activity / protein serine/threonine kinase activator activity / protein serine/threonine kinase binding / kinase binding / secretory granule lumen / ficolin-1-rich granule lumen / intracellular signal transduction / Neutrophil degranulation / extracellular exosome / extracellular region / cytosol / cytoplasm
Similarity search - Function
Mo25-like / Mo25-like / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Alpha Horseshoe / Armadillo-like helical / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Calcium-binding protein 39
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsMilburn, C.C. / Boudeau, J. / Deak, M. / Alessi, D.R. / Van Aalten, D.M.F.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Crystal Structure of Mo25 Alpha in Complex with the C-Terminus of the Pseudo Kinase Ste-20 Related Adaptor (Strad)
Authors: Milburn, C.C. / Boudeau, J. / Deak, M. / Alessi, D.R. / Van Aalten, D.M.F.
History
DepositionOct 7, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 10, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / 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_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MO25 PROTEIN
B: MO25 PROTEIN


Theoretical massNumber of molelcules
Total (without water)80,6902
Polymers80,6902
Non-polymers00
Water21612
1
A: MO25 PROTEIN


Theoretical massNumber of molelcules
Total (without water)40,3451
Polymers40,3451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MO25 PROTEIN


Theoretical massNumber of molelcules
Total (without water)40,3451
Polymers40,3451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.625, 94.012, 96.327
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MO25 PROTEIN / MO25 ALPHA / CGI 66


Mass: 40344.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): B834 / References: UniProt: Q9Y376
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
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 Å3/Da / Density % sol: 38 %
Crystal growpH: 6.5
Details: 15 % PEG 20000, 0.1 M MES PH 6.5, 4.4 % GAMMA BUTYROLACTONE
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails (eV)
114.5 mg/mlprotein1drop
215 %(w/v)PEG200001reservoir
30.1 %MES1reservoirpH6.5
440 %(v/v)gamma-butyrolactone1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.933
DetectorType: ADSC Q4 CCD / Detector: CCD / Date: Feb 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 20073 / % possible obs: 98.6 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 16.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 2.7 / % possible all: 90.6
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 30 Å / Redundancy: 5.3 % / Num. measured all: 106613 / Rmerge(I) obs: 0.118
Reflection shell
*PLUS
% possible obs: 90.6 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRY 1UPK

1upk


Resolution: 2.6→25 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.895 / SU B: 13.8 / SU ML: 0.301 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28 524 2.6 %RANDOM
Rwork0.212 ---
obs0.214 19496 98.6 %-
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: 18.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.29 Å20 Å20 Å2
2--4.08 Å20 Å2
3----1.79 Å2
Refinement stepCycle: LAST / Resolution: 2.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5107 0 0 12 5119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225075
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.9656842
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8823612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.90815972
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1180.2788
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023742
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2930.32487
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.5224
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3010.361
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4750.56
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1971.43082
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.16124968
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0342.31993
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.291.71874
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: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.308 35
Rwork0.221 1269
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)
13.3924-1.18680.0552.4145-0.75451.4803-0.0764-0.24070.42850.11490.107-0.0554-0.0227-0.0644-0.03050.2331-0.05780.02910.1918-0.11760.239213.663133.187829.0017
22.0134-0.3794-1.36312.2749-0.66581.5703-0.0258-0.20240.08060.1359-0.0138-0.0744-0.09730.07210.03960.2447-0.03230.00890.2249-0.03420.200619.242424.279625.185
31.5693-0.4635-0.25232.4035-0.17861.65-0.0211-0.04280.06260.1226-0.1751-0.00470.0203-0.03310.19620.2267-0.01390.02150.2444-0.02710.221822.20817.039816.6918
42.1592-0.8819-0.71673.195-0.07071.4317-0.0033-0.00680.0302-0.0762-0.0642-0.0505-0.0685-0.15230.06750.2295-0.02780.0030.221-0.00850.195628.607610.911210.8544
52.74310.0136-0.35042.0818-0.99832.3888-0.0492-0.052-0.0432-0.04670.03160.0581-0.0114-0.0880.01760.2312-0.0022-0.00850.1858-0.00760.219836.09034.65845.3494
62.26690.04980.24954.68290.68770.54830.1197-0.1076-0.0460.0607-0.0965-0.00450.170.0339-0.02310.27060.0240.01360.19130.0140.21945.73330.5197-1.5438
74.57232.97032.650413.24363.29233.52440.20030.005-0.4230.3439-0.2221-0.73210.04480.10080.02180.07140.0022-0.02050.21870.03830.270556.95012.7775-0.165
86.0761-3.3835-0.66794.69430.31681.7976-0.0047-0.29760.33210.36620.0859-0.0452-0.3570.1633-0.08120.2705-0.0230.02330.1626-0.05850.182144.570948.300998.7397
92.11590.32210.40071.68350.812-0.24530.06710.11460.07390.0958-0.18180.04530.01990.14540.11470.25040.0152-0.0040.1509-0.02040.232640.271343.137189.8982
101.95971.3136-0.19620.35330.84861.4073-0.06970.09-0.0374-0.05630.1450.01840.08010.0412-0.07530.21030.01690.00120.2521-0.00130.252237.59934.878483.0536
111.60230.19741.38371.6580.86843.02450.01060.08120.0130.18010.103-0.109-0.00720.0405-0.11360.20370.0011-0.00650.20960.03760.235231.179328.757675.9846
122.63471.0570.7691.65660.20721.95310.0079-0.0412-0.01250.0572-0.09050.01980.13130.12850.08260.21790.00750.00180.2059-0.00130.223523.848624.02869.6912
131.58150.30670.63962.1631-0.64466.1199-0.14990.09950.0745-0.1011-0.10510.15310.4992-0.32490.2550.248-0.05330.01310.1933-0.04880.232114.29717.713664.146
143.8901-0.3536-2.98914.38382.45529.0801-0.17610.01370.35360.0442-0.11680.37930.261-0.57030.29290.0128-0.05230.0220.215-0.07110.30263.358420.31365.9903
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 78
2X-RAY DIFFRACTION2A79 - 124
3X-RAY DIFFRACTION3A125 - 164
4X-RAY DIFFRACTION4A165 - 208
5X-RAY DIFFRACTION5A209 - 253
6X-RAY DIFFRACTION6A254 - 298
7X-RAY DIFFRACTION7A299 - 333
8X-RAY DIFFRACTION8B13 - 78
9X-RAY DIFFRACTION9B79 - 124
10X-RAY DIFFRACTION10B125 - 164
11X-RAY DIFFRACTION11B165 - 208
12X-RAY DIFFRACTION12B209 - 253
13X-RAY DIFFRACTION13B254 - 298
14X-RAY DIFFRACTION14B299 - 333
Refinement
*PLUS
Rfactor Rfree: 0.279
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.019
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.9

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