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- PDB-3la6: Octameric kinase domain of the E. coli tyrosine kinase Wzc with b... -

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Basic information

Entry
Database: PDB / ID: 3la6
TitleOctameric kinase domain of the E. coli tyrosine kinase Wzc with bound ADP
ComponentsTyrosine-protein kinase wzc
KeywordsTRANSFERASE / P-loop protein / nucleotide binding domain / Walker A motif / bacterial protein kinase / oligomerization / intermolecular phosphorylation / exopolysaccharide synthesis
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups; Protein-tyrosine kinases / colanic acid biosynthetic process / lipopolysaccharide biosynthetic process / extracellular polysaccharide biosynthetic process / plasma membrane => GO:0005886 / peptidyl-tyrosine autophosphorylation / protein tyrosine kinase activity / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Tyrosine kinase, G-rich domain / G-rich domain on putative tyrosine kinase / Exopolysaccharide synthesis protein / Polysaccharide chain length determinant N-terminal domain / Chain length determinant protein / AAA domain / AAA domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold ...Tyrosine kinase, G-rich domain / G-rich domain on putative tyrosine kinase / Exopolysaccharide synthesis protein / Polysaccharide chain length determinant N-terminal domain / Chain length determinant protein / AAA domain / AAA domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Tyrosine-protein kinase wzc
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsGruszczyk, J. / Nessler, S. / Gueguen-Chaignon, V. / Vigouroux, A. / Bechet, E. / Grangeasse, C.
CitationJournal: Mol.Microbiol. / Year: 2010
Title: Identification of structural and molecular determinants of the tyrosine-kinase Wzc and implications in capsular polysaccharide export
Authors: Bechet, E. / Gruszczyk, J. / Terreux, R. / Gueguen-Chaignon, V. / Vigouroux, A. / Obadia, B. / Cozzone, A.J. / Nessler, S. / Grangeasse, C.
History
DepositionJan 6, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Nov 1, 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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein kinase wzc
B: Tyrosine-protein kinase wzc
C: Tyrosine-protein kinase wzc
D: Tyrosine-protein kinase wzc
E: Tyrosine-protein kinase wzc
F: Tyrosine-protein kinase wzc
G: Tyrosine-protein kinase wzc
H: Tyrosine-protein kinase wzc
I: Tyrosine-protein kinase wzc
J: Tyrosine-protein kinase wzc
K: Tyrosine-protein kinase wzc
L: Tyrosine-protein kinase wzc
M: Tyrosine-protein kinase wzc
N: Tyrosine-protein kinase wzc
O: Tyrosine-protein kinase wzc
P: Tyrosine-protein kinase wzc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)514,36148
Polymers506,88416
Non-polymers7,47632
Water00
1
A: Tyrosine-protein kinase wzc
B: Tyrosine-protein kinase wzc
C: Tyrosine-protein kinase wzc
D: Tyrosine-protein kinase wzc
E: Tyrosine-protein kinase wzc
F: Tyrosine-protein kinase wzc
G: Tyrosine-protein kinase wzc
H: Tyrosine-protein kinase wzc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,18024
Polymers253,4428
Non-polymers3,73816
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21210 Å2
ΔGint-38 kcal/mol
Surface area75830 Å2
MethodPISA
2
I: Tyrosine-protein kinase wzc
J: Tyrosine-protein kinase wzc
K: Tyrosine-protein kinase wzc
L: Tyrosine-protein kinase wzc
M: Tyrosine-protein kinase wzc
N: Tyrosine-protein kinase wzc
O: Tyrosine-protein kinase wzc
P: Tyrosine-protein kinase wzc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,18024
Polymers253,4428
Non-polymers3,73816
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20910 Å2
ΔGint-45 kcal/mol
Surface area74700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)245.165, 137.782, 158.958
Angle α, β, γ (deg.)90.000, 92.990, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Tyrosine-protein kinase wzc


Mass: 31680.266 Da / Num. of mol.: 16 / Fragment: Cytoplasmic domain, UNP RESIDUES 447-720
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2060, JW2045, wzc / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15(pREP4)
References: UniProt: P76387, Transferases; Transferring phosphorus-containing groups; Protein-tyrosine kinases
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
Sequence detailsRESIDUE K540M IS MUTAGENESIS ACCORDING TO DATABASE UNIPROTKB/SWISS-PROT P76387 (WZC_ECOLI).

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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: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 290 K / pH: 7.5
Details: 14% PEG 4000, 0.1M Hepes, 0.1M NaCl, 0.15M CaCl2, 20% NaI 1.0M, pH 7.5, VAPOR DIFFUSION, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3.2→158.742 Å / Num. obs: 83937 / % possible obs: 96.5 % / Redundancy: 2.5 % / Biso Wilson estimate: 103.54 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 11.1
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 1.2 / Rsym value: 0.526 / % possible all: 97.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 56.69 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.2 Å49.74 Å
Translation3.2 Å49.74 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASER2.1.1phasing
TNTrefinement
PDB_EXTRACT3.005data extraction
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VED

2ved


Resolution: 3.2→49.74 Å / Cor.coef. Fo:Fc: 0.9296 / Cor.coef. Fo:Fc free: 0.9051 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
Details: The structure was also refined with NCS using PHENIX-1.4-3.
RfactorNum. reflection% reflectionSelection details
Rfree0.2234 833 0.99 %RANDOM
Rwork0.1859 ---
obs0.1863 83934 --
Displacement parametersBiso mean: 83.73 Å2
Baniso -1Baniso -2Baniso -3
1-8.7076 Å20 Å28.7173 Å2
2---10.1545 Å20 Å2
3---1.4469 Å2
Refine analyzeLuzzati coordinate error obs: 0.56 Å
Refinement stepCycle: LAST / Resolution: 3.2→49.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31972 0 448 0 32420
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0132980HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2844881HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d11492SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes886HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4703HARMONIC5
X-RAY DIFFRACTIONt_it32980HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 3.2→3.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2581 66 1.05 %
Rwork0.2351 6201 -
all0.2353 6267 -

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