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- PDB-4jlv: Crystal structure of the chimerical protein CapA1B1 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4jlv
TitleCrystal structure of the chimerical protein CapA1B1 in complex with ADP-Mg
ComponentsC-terminal fragment of Membrane protein CapA1, Putative uncharacterized protein capB1
KeywordsTRANSFERASE / Rossmann fold / tyrosine kinase / ATP-binding
Function / homology
Function and homology information


polysaccharide transport / carbohydrate:proton symporter activity / polysaccharide biosynthetic process / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / protein tyrosine kinase activity / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Polysaccharide export protein MPA1-like / Exopolysaccharide synthesis protein / Polysaccharide chain length determinant N-terminal domain / Chain length determinant protein / : / AAA domain / AAA domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase ...Polysaccharide export protein MPA1-like / Exopolysaccharide synthesis protein / Polysaccharide chain length determinant N-terminal domain / Chain length determinant protein / : / AAA domain / AAA domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Capsular biosynthesis protein / non-specific protein-tyrosine kinase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGruszczyk, J. / Olivares-Illana, V. / Nourikyan, J. / Fleurie, A. / Bechet, E. / Aumont-Nicaise, M. / Gueguen-Chaignon, V. / Morera, S. / Grangeasse, C. / Nessler, S.
CitationJournal: Plos One / Year: 2013
Title: Comparative analysis of the Tyr-kinases CapB1 and CapB2 fused to their cognate modulators CapA1 and CapA2 from Staphylococcus aureus
Authors: Gruszczyk, J. / Olivares-Illana, V. / Nourikyan, J. / Fleurie, A. / Bechet, E. / Gueguen-Chaignon, V. / Freton, C. / Aumont-Nicaise, M. / Morera, S. / Grangeasse, C. / Nessler, S.
History
DepositionMar 13, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector
Revision 1.2Nov 8, 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_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.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_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_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

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Assembly

Deposited unit
A: C-terminal fragment of Membrane protein CapA1, Putative uncharacterized protein capB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5483
Polymers30,0961
Non-polymers4522
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.030, 64.630, 88.280
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 C-terminal fragment of Membrane protein CapA1, Putative uncharacterized protein capB1


Mass: 30096.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Chimera of Membrane protein CapA1 and tyrosine kinase CapB1
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: capA1, capB1 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: A8YPQ6, UniProt: A8YPQ8
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 23 / 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: 1.94 Å3/Da / Density % sol: 36.74 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 8.5
Details: 28% PEG 1000, 100mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 26, 2008
RadiationMonochromator: cooled channel-cut Si(311) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 12422 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.752 %
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 4.81 % / Rmerge(I) obs: 1.113 / Mean I/σ(I) obs: 1.93 / Num. unique all: 1515 / Rsym value: 1.252 / % possible all: 99.5

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BFV

3bfv


Resolution: 2.2→44.14 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7625 / SU ML: 0.25 / σ(F): 1.36 / Phase error: 29.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.242 621 5.01 %random
Rwork0.1972 ---
obs0.1994 12399 99.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.71 Å2 / Biso mean: 57.5635 Å2 / Biso min: 35.93 Å2
Refinement stepCycle: LAST / Resolution: 2.2→44.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1774 0 28 23 1825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081823
X-RAY DIFFRACTIONf_angle_d1.2122463
X-RAY DIFFRACTIONf_chiral_restr0.073293
X-RAY DIFFRACTIONf_plane_restr0.005310
X-RAY DIFFRACTIONf_dihedral_angle_d15.617706
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2005-2.42190.32711520.26872884303699
2.4219-2.77230.31131530.236829003053100
2.7723-3.49260.28741550.206429423097100
3.4926-44.14890.19131610.173052321399

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