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- PDB-4kuj: Structural and functional characterization of a novel Alpha Kinas... -

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Basic information

Entry
Database: PDB / ID: 4kuj
TitleStructural and functional characterization of a novel Alpha Kinase from Entamoeba histolytica
ComponentsProtein kinase, putative
KeywordsTRANSFERASE / Actin / Phosphorylated actin / Phosphorylation
Function / homology
Function and homology information


cellular component assembly / protein serine/threonine kinase activity / ATP binding / metal ion binding
Similarity search - Function
Protein kinase-like fold / MHCK/EF2 kinase / : / MHCK/EF2 kinase / Alpha-kinase family / Alpha-type protein kinase domain profile. / Alpha-kinase family / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily ...Protein kinase-like fold / MHCK/EF2 kinase / : / MHCK/EF2 kinase / Alpha-kinase family / Alpha-type protein kinase domain profile. / Alpha-kinase family / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Alpha-Beta Barrel / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Protein kinase, putative
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsRehman, S.A.A. / Tarique, K.F. / Bhattacharya, A. / Gourinath, S. / Mansuri, M.S.
CitationJournal: To be Published
Title: Structural and functional characterization of a novel Alpha Kinase from Entamoeba histolytica
Authors: Rehman, S.A.A. / Tarique, K.F. / Bhattacharya, A. / Gourinath, S. / Mansuri, M.S.
History
DepositionMay 22, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_asym_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_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein kinase, putative
B: Protein kinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2715
Polymers67,0342
Non-polymers2373
Water2,648147
1
A: Protein kinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6893
Polymers33,5171
Non-polymers1722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein kinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5822
Polymers33,5171
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Protein kinase, putative
hetero molecules

B: Protein kinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2715
Polymers67,0342
Non-polymers2373
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1/2,-y,z-1/21
Buried area2090 Å2
ΔGint-4 kcal/mol
Surface area23980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.057, 89.634, 122.920
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 Protein kinase, putative


Mass: 33516.984 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1, IMSS-B / Gene: EHI8A_073090 / Plasmid: pET(28b) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: M3TP73
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.1 Å3/Da / Density % sol: 41.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 3350, Tris pH7.5, 150mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.953 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. all: 39003 / Num. obs: 36985 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 21.57
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 2.88 / Num. unique all: 1896 / % possible all: 97.2

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.156 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2391 1955 5 %RANDOM
Rwork0.20889 ---
obs0.21039 36985 99.13 %-
all-39003 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.287 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20 Å2
2---0.54 Å20 Å2
3---1.03 Å2
Refine analyzeLuzzati coordinate error obs: 0.242 Å
Refinement stepCycle: LAST / Resolution: 1.99→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4328 0 9 147 4484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.024447
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.9436044
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0045529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43924.26223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.53815734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.4951522
X-RAY DIFFRACTIONr_chiral_restr0.10.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213396
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.994→2.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 131 -
Rwork0.252 2341 -
obs--92.1 %

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