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- PDB-4pf4: 1.1A X-RAY STRUCTURE OF THE APO CATALYTIC DOMAIN OF DEATH-ASSOCIA... -

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Basic information

Entry
Database: PDB / ID: 4pf4
Title1.1A X-RAY STRUCTURE OF THE APO CATALYTIC DOMAIN OF DEATH-ASSOCIATED PROTEIN KINASE 1, aa 1-277
ComponentsDeath-associated protein kinase 1DAPK1
KeywordsTRANSFERASE
Function / homology
Function and homology information


cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / syntaxin-1 binding / regulation of NMDA receptor activity / calmodulin-dependent protein kinase activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process ...cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / syntaxin-1 binding / regulation of NMDA receptor activity / calmodulin-dependent protein kinase activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of autophagy / regulation of autophagy / apoptotic signaling pathway / cellular response to type II interferon / actin cytoskeleton / regulation of apoptotic process / protein autophosphorylation / postsynaptic density / negative regulation of translation / calmodulin binding / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / GTP binding / negative regulation of apoptotic process / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Death-associated protein kinase 1 / Roc domain profile. / Roc domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) ...Death-associated protein kinase 1 / Roc domain profile. / Roc domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Death-associated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.13 Å
AuthorsTemmerman, K. / Simon, B. / Wilmanns, M.
CitationJournal: To Be Published
Title: 1.1A X-RAY STRUCTURE OF THE APO CATALYTIC DOMAIN OF DEATH-ASSOCIATED PROTEIN KINASE 1, aa 1-277
Authors: Temmerman, K. / Simon, B. / Wilmanns, M.
History
DepositionApr 28, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references / Structure summary
Revision 1.2Dec 20, 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_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_asym_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Death-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,99814
Polymers31,9901
Non-polymers1,00713
Water8,809489
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-75 kcal/mol
Surface area13780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.516, 62.005, 88.375
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Death-associated protein kinase 1 / DAPK1 / DAP kinase 1


Mass: 31990.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAPK1, DAPK / Plasmid: pnEA-vHisGST / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Rosetta2
References: UniProt: P53355, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 502 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 1.99 Å3/Da / Density % sol: 38.25 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES, Ph=7, 2M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.973 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 6, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 1.129→50.758 Å / Num. all: 96009 / Num. obs: 96009 / % possible obs: 99.4 % / Redundancy: 6.3 % / Rpim(I) all: 0.032 / Rrim(I) all: 0.082 / Rsym value: 0.076 / Net I/av σ(I): 5.944 / Net I/σ(I): 10.7 / Num. measured all: 601419
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.13-1.1950.7091.167334134310.3410.709296.5
1.19-1.266.30.5581.482580131670.2380.558399.8
1.26-1.356.30.382278525124250.1630.3824.2100
1.35-1.466.50.2692.875316115670.1130.2695.8100
1.46-1.66.40.1694.468995107010.0710.1698.6100
1.6-1.796.70.1096.76464397160.0450.10912.5100
1.79-2.066.60.07105637185960.0290.0718.4100
2.06-2.526.70.05512.44887873190.0230.05525100
2.52-3.576.60.04813.23799357700.020.04830.6100
3.57-50.7586.30.04214.62078433170.0180.04234.599.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation50.76 Å1.47 Å

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
MOLREP11.0.05phasing
PDB_EXTRACT3.14data extraction
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W4J

2w4j


Resolution: 1.13→50.758 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.978 / WRfactor Rfree: 0.1467 / WRfactor Rwork: 0.1134 / FOM work R set: 0.9154 / SU B: 1.024 / SU ML: 0.021 / SU R Cruickshank DPI: 0.0284 / SU Rfree: 0.0307 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.028 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1495 4805 5 %RANDOM
Rwork0.1167 91109 --
obs0.1183 95914 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 144.22 Å2 / Biso mean: 16.198 Å2 / Biso min: 5.94 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20 Å20 Å2
2--0.61 Å20 Å2
3---0.49 Å2
Refinement stepCycle: final / Resolution: 1.13→50.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2232 0 107 489 2828
Biso mean--45.63 33.44 -
Num. residues----278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0192470
X-RAY DIFFRACTIONr_bond_other_d0.0020.022412
X-RAY DIFFRACTIONr_angle_refined_deg2.1841.9853350
X-RAY DIFFRACTIONr_angle_other_deg2.16835511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1645307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20424.783115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90715447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6111512
X-RAY DIFFRACTIONr_chiral_restr0.1630.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212793
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02549
X-RAY DIFFRACTIONr_rigid_bond_restr6.95534882
X-RAY DIFFRACTIONr_sphericity_free36.855570
X-RAY DIFFRACTIONr_sphericity_bonded17.94355252
LS refinement shellResolution: 1.129→1.158 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 319 -
Rwork0.272 6304 -
all-6623 -
obs--94.09 %

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