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- PDB-4da1: Crystal structure of branched-chain alpha-ketoacid dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 4da1
TitleCrystal structure of branched-chain alpha-ketoacid dehydrogenase phosphatase with Mg (II) ions at the active site
ComponentsProtein phosphatase 1K, mitochondrial
KeywordsHYDROLASE / metal-ion-assisted catalysis / dehydrogenase phosphatase / mitochondria
Function / homology
Function and homology information


[3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)]-phosphatase / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / regulation of mitochondrial membrane permeability involved in apoptotic process / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / manganese ion binding / mitochondrial matrix / mitochondrion ...[3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)]-phosphatase / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / regulation of mitochondrial membrane permeability involved in apoptotic process / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / manganese ion binding / mitochondrial matrix / mitochondrion / nucleus / cytosol
Similarity search - Function
Sigma factor PP2C-like phosphatases / PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Protein phosphatase 2C / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain ...Sigma factor PP2C-like phosphatases / PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Protein phosphatase 2C / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Protein phosphatase Mn(2+)-dependent 1K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.383 Å
AuthorsBrautigam, C.A. / Chuang, J.L. / Chuang, D.T.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural and biochemical characterization of human mitochondrial branched-chain alpha-ketoacid dehydrogenase phosphatase.
Authors: Wynn, R.M. / Li, J. / Brautigam, C.A. / Chuang, J.L. / Chuang, D.T.
History
DepositionJan 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_type.id / _struct_ref_seq_dif.details / _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: Protein phosphatase 1K, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6467
Polymers43,3391
Non-polymers3076
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.276, 125.276, 61.660
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Protein phosphatase 1K, mitochondrial / PP2C domain-containing protein phosphatase 1K / PP2C-like mitochondrial protein / PP2C-type ...PP2C domain-containing protein phosphatase 1K / PP2C-like mitochondrial protein / PP2C-type mitochondrial phosphoprotein phosphatase / PTMP / Protein phosphatase 2C isoform kappa / PP2C-kappa


Mass: 43338.805 Da / Num. of mol.: 1
Fragment: truncated phosphatase protein (UNP residues 84-360)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPM1K, PP2CM / Production host: Escherichia coli (E. coli)
References: UniProt: Q8N3J5, protein-serine/threonine phosphatase
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 3.22 Å3/Da / Density % sol: 61.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, 19% PEG3350, 0.2 M Magnesium chloride, 20 mM beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2010
RadiationMonochromator: Sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 22452 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 42.04 Å2
Reflection shellResolution: 2.38→2.42 Å / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
SBC-CollectCOLLECTdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IQ1

2iq1


Resolution: 2.383→43.942 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.61 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2049 1146 5.11 %RANDOM
Rwork0.1769 ---
obs0.1783 22432 99.55 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.287 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso max: 136.34 Å2 / Biso mean: 51.3423 Å2 / Biso min: 23.08 Å2
Baniso -1Baniso -2Baniso -3
1-6.7034 Å20 Å2-0 Å2
2--6.7034 Å20 Å2
3----13.4068 Å2
Refinement stepCycle: LAST / Resolution: 2.383→43.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1980 0 15 64 2059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082027
X-RAY DIFFRACTIONf_angle_d1.072736
X-RAY DIFFRACTIONf_chiral_restr0.069314
X-RAY DIFFRACTIONf_plane_restr0.004355
X-RAY DIFFRACTIONf_dihedral_angle_d15.766741
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3833-2.49180.30551330.26852610274399
2.4918-2.62310.27531420.233826452787100
2.6231-2.78740.23511400.213726682808100
2.7874-3.00260.26091410.199126232764100
3.0026-3.30470.21431440.192726562800100
3.3047-3.78260.21131600.172726552815100
3.7826-4.76480.1821550.14232676283199
4.7648-43.94930.15771310.15872753288499
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)
13.90380.4435-0.50794.08391.58792.3055-0.0508-0.0057-0.1163-0.3251-0.0305-0.2440.14680.57740.05620.3920.11950.0190.25880.07540.32417.736128.3515-84.9516
22.1603-0.37120.58362.9711-1.06482.75630.051-0.0985-0.3910.0921-0.1091-0.02720.6386-0.11450.01370.44790.02870.0530.17940.03080.34327.8756117.1614-80.8487
33.44971.67560.81472.7276-2.24846.81730.16040.04490.09490.06260.05460.2679-0.2016-0.0001-0.22680.28140.08670.02850.1768-0.00260.25581.3107131.7627-88.7858
43.4326-0.5726-0.15812.46331.02638.6532-0.0847-0.34540.21570.41560.10440.3105-0.2089-0.3614-0.00620.25640.0180.07740.1607-0.010.3314-2.2021128.4711-75.7893
55.44191.69011.56127.58722.07537.0893-0.1380.12980.317-0.3891-0.1123-0.1275-0.5390.23850.24290.29640.02570.02280.20650.05710.265213.2823139.1928-88.5254
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 90:117)A90 - 117
2X-RAY DIFFRACTION2chain 'A' and (resseq 118:196)A118 - 196
3X-RAY DIFFRACTION3chain 'A' and (resseq 197:230)A197 - 230
4X-RAY DIFFRACTION4chain 'A' and (resseq 231:290)A231 - 290
5X-RAY DIFFRACTION5chain 'A' and (resseq 291:348)A291 - 348

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