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- PDB-3bfv: crystal structure of the chimerical protein CapAB -

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Basic information

Entry
Database: PDB / ID: 3bfv
Titlecrystal structure of the chimerical protein CapAB
ComponentsMembrane protein CapA1, Protein tyrosine kinase,Protein tyrosine kinaseBiological membrane
KeywordsTRANSFERASE / chimerical protein / P-loop protein / Capsule biogenesis/degradation / Exopolysaccharide synthesis / Membrane / Transmembrane / Virulence
Function / homology
Function and homology information


carbohydrate:proton symporter activity / polysaccharide transport / extracellular polysaccharide biosynthetic process / lipopolysaccharide biosynthetic process / : / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / kinase activity / membrane => GO:0016020 / phosphorylation ...carbohydrate:proton symporter activity / polysaccharide transport / extracellular polysaccharide biosynthetic process / lipopolysaccharide biosynthetic process / : / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / kinase activity / membrane => GO:0016020 / phosphorylation / nucleotide binding / ATP binding / plasma membrane
Similarity search - Function
Polysaccharide export protein MPA1-like / Exopolysaccharide synthesis protein / CobQ/CobB/MinD/ParA nucleotide binding domain / 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 ...Polysaccharide export protein MPA1-like / Exopolysaccharide synthesis protein / CobQ/CobB/MinD/ParA nucleotide binding domain / 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 / non-specific protein-tyrosine kinase / Capsular biosynthesis protein / Capsular polysaccharide type 8 biosynthesis protein cap8A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsOlivares-Illana, V. / Meyer, P. / Morera, S. / Nessler, S.
CitationJournal: Plos Biol. / Year: 2008
Title: Structural Basis for the Regulation Mechanism of the Tyrosine Kinase CapB from Staphylococcus aureus.
Authors: Olivares-Illana, V. / Meyer, P. / Bechet, E. / Gueguen-Chaignon, V. / Soulat, D. / Lazereg-Riquier, S. / Mijakovic, I. / Deutscher, J. / Cozzone, A.J. / Laprevote, O. / Morera, S. / Grangeasse, C. / Nessler, S.
History
DepositionNov 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 9, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Jun 13, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_pdb_strand_id / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.4Jun 27, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.5Aug 30, 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_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_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_conn.ptnr2_label_seq_id / _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: Membrane protein CapA1, Protein tyrosine kinase,Protein tyrosine kinase
B: Membrane protein CapA1, Protein tyrosine kinase,Protein tyrosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9006
Polymers59,9972
Non-polymers9034
Water7,530418
1
A: Membrane protein CapA1, Protein tyrosine kinase,Protein tyrosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4503
Polymers29,9991
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Membrane protein CapA1, Protein tyrosine kinase,Protein tyrosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4503
Polymers29,9991
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.460, 52.520, 68.110
Angle α, β, γ (deg.)107.71, 89.95, 110.32
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Membrane protein CapA1, Protein tyrosine kinase,Protein tyrosine kinase / Biological membrane


Mass: 29998.740 Da / Num. of mol.: 2
Fragment: FUSION PROTEIN CONSISTS OF UNP RESIDUES 194-222 (P72367) and 1-230 (A8YPQ5) OF CAPA1 AND CAPB2,FUSION PROTEIN CONSISTS OF UNP RESIDUES 194-222 (A8YPQ6) and 1-230 (A8YPQ5) OF CAPA1 AND CAPB2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: cap8A, capB2 / Plasmid: pQE30 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P72367, UniProt: A8YPQ5, UniProt: A8YPQ6*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.22 %
Crystal growTemperature: 298 K / pH: 8.8
Details: 23 % PEG 1000, 0.1 M Tris-HCl, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.80

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorDetector: CCD / Date: Apr 16, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
10.9SINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 39022 / % possible obs: 98.7 % / Observed criterion σ(I): 1 / Rsym value: 0.088 / Net I/σ(I): 9.35
Reflection shellResolution: 1.8→1.9 Å / Rsym value: 0.303 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1ION

1ion


Resolution: 1.8→19.94 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.914 / SU B: 2.532 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 2054 5 %RANDOM
Rwork0.178 ---
obs0.18 39022 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.48 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20.01 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3728 0 56 418 4202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223850
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.9945242
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7135480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.77225.802162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20415672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0821516
X-RAY DIFFRACTIONr_chiral_restr0.0780.2616
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022842
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1860.21827
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22731
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0940.2363
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.248
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5861.52484
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.93523934
X-RAY DIFFRACTIONr_scbond_it1.42131532
X-RAY DIFFRACTIONr_scangle_it2.2314.51308
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 152 -
Rwork0.224 2898 -
obs--100 %

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