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- PDB-4qny: Crystal structure of MapK from Leishmania donovani, LDBPK_331470 -

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Basic information

Entry
Database: PDB / ID: 4qny
TitleCrystal structure of MapK from Leishmania donovani, LDBPK_331470
ComponentsMitogen activated protein kinase, putative
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / leishmania / kinase
Function / homology
Function and homology information


protein kinase activity / ATP binding
Similarity search - Function
Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. ...Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Mitogen activated protein kinase, putative
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.257 Å
AuthorsWernimont, A.K. / Loppnau, P. / Walker, J.R. / Mangos, M. / El Bakkouri, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Amani, M. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of MapK from Leishmania donovani, LDBPK_331470
Authors: Wernimont, A.K. / Loppnau, P. / Walker, J.R. / Mangos, M. / El Bakkouri, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Amani, M.
History
DepositionJun 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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: Mitogen activated protein kinase, putative
B: Mitogen activated protein kinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0127
Polymers81,8592
Non-polymers1,1535
Water5,170287
1
A: Mitogen activated protein kinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4603
Polymers40,9301
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitogen activated protein kinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5524
Polymers40,9301
Non-polymers6233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Mitogen activated protein kinase, putative
hetero molecules

A: Mitogen activated protein kinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0127
Polymers81,8592
Non-polymers1,1535
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area3840 Å2
ΔGint-36 kcal/mol
Surface area30740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.203, 86.063, 82.066
Angle α, β, γ (deg.)90.00, 97.34, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAUTHORS HAVE INDICATED THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein Mitogen activated protein kinase, putative


Mass: 40929.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Strain: BPK282A1 / Gene: LDBK_331470, LDBPK_331470 / Plasmid: Pet15mlh / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: E9BQ78
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS HAVE DETERMINED THE CORRECT SEQUENCE BY DNA SEQUENCING.

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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: 2.4 Å3/Da / Density % sol: 48.85 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 17% PEG3350, 0.2 M MgCl2, 0.1 M Tris, 5 % glycerol, 5 mM AMPPNP, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979183 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.26→46.79 Å / Num. all: 36575 / Num. obs: 35990 / % possible obs: 98.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 23.86 Å2 / Rmerge(I) obs: 0.163 / Net I/σ(I): 7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.26-2.3340.6842.2193.9
9.03-46.793.90.06215.4198

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Processing

Software
NameVersionClassificationNB
Aimless0.2.17data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
SBC-Collectdata collection
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4b9f

4b9f


Resolution: 2.257→43.032 Å / SU ML: 0.37 / σ(F): 0.21 / Phase error: 30.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2851 1736 4.84 %
Rwork0.2343 --
obs0.2367 34234 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.3931 Å2
Refinement stepCycle: LAST / Resolution: 2.257→43.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5294 0 70 287 5651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035512
X-RAY DIFFRACTIONf_angle_d0.6387480
X-RAY DIFFRACTIONf_dihedral_angle_d14.2012029
X-RAY DIFFRACTIONf_chiral_restr0.025858
X-RAY DIFFRACTIONf_plane_restr0.003955
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2566-2.28880.33691180.3272588X-RAY DIFFRACTION89
2.2888-2.3230.37171600.30352802X-RAY DIFFRACTION99
2.323-2.35930.34711450.28972775X-RAY DIFFRACTION98
2.3593-2.3980.34971760.29732809X-RAY DIFFRACTION100
2.398-2.43930.34081540.27962814X-RAY DIFFRACTION98
2.4393-2.48370.34891230.28722795X-RAY DIFFRACTION100
2.4837-2.53140.33741080.29092911X-RAY DIFFRACTION100
2.5314-2.58310.36141300.2792788X-RAY DIFFRACTION98
2.5831-2.63930.34961580.26642830X-RAY DIFFRACTION100
2.6393-2.70060.33561650.27122806X-RAY DIFFRACTION99
2.7006-2.76820.31251350.25762851X-RAY DIFFRACTION100
2.7682-2.8430.38711440.26632791X-RAY DIFFRACTION98
2.843-2.92660.38771210.27392865X-RAY DIFFRACTION100
2.9266-3.02110.32071460.25912825X-RAY DIFFRACTION99
3.0211-3.1290.3081510.24762816X-RAY DIFFRACTION99
3.129-3.25430.27821640.22842773X-RAY DIFFRACTION100
3.2543-3.40230.26951390.21992849X-RAY DIFFRACTION99
3.4023-3.58160.31591350.21552809X-RAY DIFFRACTION99
3.5816-3.80590.25331150.19772812X-RAY DIFFRACTION98
3.8059-4.09950.22011430.19682812X-RAY DIFFRACTION98
4.0995-4.51170.19281480.18582735X-RAY DIFFRACTION97
4.5117-5.16360.24391480.17682795X-RAY DIFFRACTION98
5.1636-6.5020.24551410.21472796X-RAY DIFFRACTION99
6.502-43.03930.21531490.21512780X-RAY DIFFRACTION98
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)
12.4959-0.32130.06350.71090.8051.41370.0152-0.0007-0.25540.02920.0321-0.1665-0.05440.0755-0.05730.2286-0.0215-0.01960.19380.09170.311727.548739.347422.6907
21.5052-0.0738-0.13111.960.53350.37610.06960.0451-0.1472-0.0933-0.07460.0147-0.00740.06380.00830.152-0.01030.01630.19850.0160.13313.902147.662315.6122
32.239-0.16310.3151.20480.41160.45990.0499-0.0922-0.19670.0505-0.10880.18870.09-0.01980.05630.1777-0.04960.03570.19970.02930.13440.35442.844120.3913
42.7372-0.67310.20251.8845-0.76491.7434-0.032-0.17070.42240.04790.16360.12370.0168-0.0977-0.13830.1901-0.007-0.00470.2469-0.02940.3153-10.77043.946722.4794
52.75710.1272-0.32630.7151-0.22650.7292-0.006-0.22070.4690.00410.06930.0729-0.0966-0.0749-0.07410.24650.0022-0.05610.2157-0.02520.27313.92326.531320.5939
61.71650.0867-0.30181.8270.68030.5156-0.1436-0.23920.13640.2670.1953-0.01870.1151-0.2161-0.04490.2267-0.0238-0.05240.20330.02780.201511.7594-7.293520.1677
71.48620.90310.68114.275-0.01810.5980.01540.07760.00120.0059-0.0478-0.28960.03030.10280.0470.1454-0.00340.01820.22440.01290.223.8635-5.715414.2472
83.05761.3838-0.25831.3537-0.22730.01460.2118-0.48340.1120.1041-0.3637-0.2555-0.2778-0.1304-0.04130.34010.07440.11460.516-0.16820.0459-3.3223-1.311837.026
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 105 )
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 263 )
3X-RAY DIFFRACTION3chain 'A' and (resid 264 through 350 )
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 76 )
5X-RAY DIFFRACTION5chain 'B' and (resid 77 through 162 )
6X-RAY DIFFRACTION6chain 'B' and (resid 163 through 218 )
7X-RAY DIFFRACTION7chain 'B' and (resid 219 through 318 )
8X-RAY DIFFRACTION8chain 'B' and (resid 319 through 350 )

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