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- PDB-3nie: Crystal Structure of PF11_0147 -

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Basic information

Entry
Database: PDB / ID: 3nie
TitleCrystal Structure of PF11_0147
ComponentsMAP2 kinase
KeywordsTRANSFERASE / malaria / MapK / kinase / SGC / Structural Genomics Consortium / structural genomics
Function / homology
Function and homology information


RAF-independent MAPK1/3 activation / Frs2-mediated activation / : / : / Signalling to ERK5 / ERKs are inactivated / : / : / Ca2+ pathway / VEGFA-VEGFR2 Pathway ...RAF-independent MAPK1/3 activation / Frs2-mediated activation / : / : / Signalling to ERK5 / ERKs are inactivated / : / : / Ca2+ pathway / VEGFA-VEGFR2 Pathway / : / : / RAF/MAP kinase cascade / Negative regulation of MAPK pathway / : / MAPK6/MAPK4 signaling / Neutrophil degranulation / MAP kinase activity / mitogen-activated protein kinase / MAPK cascade / regulation of gene expression / intracellular signal transduction / protein phosphorylation / signal transduction / ATP binding / nucleus / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / 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 ...Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Mitogen-activated protein kinase / Mitogen-activated protein kinase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWernimont, A.K. / Hutchinson, A. / Sullivan, H. / MacKenzie, F. / Kozieradzki, I. / Chau, I. / Lew, J. / Senisterra, G. / Cossar, D. / Amani, M. ...Wernimont, A.K. / Hutchinson, A. / Sullivan, H. / MacKenzie, F. / Kozieradzki, I. / Chau, I. / Lew, J. / Senisterra, G. / Cossar, D. / Amani, M. / Artz, J.D. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Hui, R. / Hills, T. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of PF11_0147
Authors: Wernimont, A.K. / Hutchinson, A. / Sullivan, H. / MacKenzie, F. / Kozieradzki, I. / Chau, I. / Lew, J. / Senisterra, G. / Cossar, D. / Amani, M. / Artz, J.D. / Bochkarev, A. / Arrowsmith, C. ...Authors: Wernimont, A.K. / Hutchinson, A. / Sullivan, H. / MacKenzie, F. / Kozieradzki, I. / Chau, I. / Lew, J. / Senisterra, G. / Cossar, D. / Amani, M. / Artz, J.D. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Hui, R. / Hills, T.
History
DepositionJun 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 20, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 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 / 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 / _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: MAP2 kinase
B: MAP2 kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,3104
Polymers100,2982
Non-polymers1,0122
Water1,54986
1
A: MAP2 kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6552
Polymers50,1491
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MAP2 kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6552
Polymers50,1491
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-23 kcal/mol
Surface area31260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.388, 107.355, 70.787
Angle α, β, γ (deg.)90.000, 109.650, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MAP2 kinase


Mass: 50148.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: map2 / Plasmid: PEt15mlh / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: Q9GR08, UniProt: Q7KQK7*PLUS
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 22% PEG 3350, 0.175 M disodium tartrate, 2 mM AMPPNP, 4 mM MgCl2, 2 mM TCEP, 20% glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: May 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 39641 / Num. obs: 37818 / % possible obs: 95.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 53.2 Å2 / Rmerge(I) obs: 0.05 / Χ2: 0.432 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.3430.33817190.209185.7
2.34-2.383.20.3117580.221190.3
2.38-2.433.40.32518390.221192.1
2.43-2.483.50.28618350.216194.3
2.48-2.533.60.26218940.237194.3
2.53-2.593.70.24918440.234195.3
2.59-2.663.80.20618860.255194.8
2.66-2.733.80.18519010.28195.9
2.73-2.813.90.15718620.285195.5
2.81-2.93.90.13119030.301195.7
2.9-33.90.11318990.359196.2
3-3.123.90.09619120.399196.6
3.12-3.263.90.07819060.45196.6
3.26-3.443.90.06219060.466197.1
3.44-3.653.90.05219380.587197.1
3.65-3.933.80.04419470.604197.3
3.93-4.333.80.0419200.751198.1
4.33-4.953.80.03519740.753198.2
4.95-6.243.80.03219640.642198.6
6.24-503.60.02820110.919198.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3N9X

3n9x


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.2537 / WRfactor Rwork: 0.2141 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.788 / SU B: 9.172 / SU ML: 0.219 / SU R Cruickshank DPI: 0.3744 / SU Rfree: 0.2602 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2681 1906 5 %RANDOM
Rwork0.2231 ---
obs0.2254 37792 95.02 %-
all-39772 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 85.05 Å2 / Biso mean: 48.6944 Å2 / Biso min: 20.47 Å2
Baniso -1Baniso -2Baniso -3
1--5.06 Å20 Å2-0.53 Å2
2--3.96 Å20 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5808 0 62 86 5956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226011
X-RAY DIFFRACTIONr_bond_other_d0.0010.023978
X-RAY DIFFRACTIONr_angle_refined_deg1.281.9828178
X-RAY DIFFRACTIONr_angle_other_deg0.86339740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8635733
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7624.291261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.197151022
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3231530
X-RAY DIFFRACTIONr_chiral_restr0.070.2952
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216562
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021196
X-RAY DIFFRACTIONr_mcbond_it0.6011.53692
X-RAY DIFFRACTIONr_mcbond_other0.0891.51467
X-RAY DIFFRACTIONr_mcangle_it1.11225974
X-RAY DIFFRACTIONr_scbond_it1.36132319
X-RAY DIFFRACTIONr_scangle_it2.2134.52204
LS refinement shellResolution: 2.3→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 110 -
Rwork0.349 2298 -
all-2408 -
obs-1719 81.41 %

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