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- PDB-4ci6: Mechanisms of crippling actin-dependent phagocytosis by YopO -

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Basic information

Entry
Database: PDB / ID: 4ci6
TitleMechanisms of crippling actin-dependent phagocytosis by YopO
Components
  • ACTIN
  • PROTEIN KINASE YOPO
KeywordsTRANSFERASE/STRUCTURAL PROTEIN / TRANSFERASE-STRUCTURAL PROTEIN COMPLEX / BUBONIC PLAGUE
Function / homology
Function and homology information


non-specific serine/threonine protein kinase / phosphorylation / protein serine/threonine kinase activity / ATP binding
Similarity search - Function
Serine/threonine protein kinase, yersinia-type / YpkA, Rac1-binding domain / Rac1-binding domain, C-terminal / Rac1-binding domain, N-terminal / Rac1-binding domain / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site ...Serine/threonine protein kinase, yersinia-type / YpkA, Rac1-binding domain / Rac1-binding domain, C-terminal / Rac1-binding domain, N-terminal / Rac1-binding domain / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Actin / YopO
Similarity search - Component
Biological speciesYERSINIA ENTEROCOLITICA (bacteria)
SPODOPTERA FRUGIPERDA (fall armyworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.651 Å
AuthorsLee, W.L. / Grimes, J.M. / Robinson, R.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Yersinia Effector Yopo Uses Actin as Bait to Phosphorylate Proteins that Regulate Actin Polymerization.
Authors: Lee, W.L. / Grimes, J.M. / Robinson, R.C.
History
DepositionDec 6, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Mar 4, 2015Group: Database references
Revision 1.3Mar 18, 2015Group: Database references
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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: ACTIN
B: PROTEIN KINASE YOPO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,0804
Polymers113,5322
Non-polymers5472
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-25.9 kcal/mol
Surface area41130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.799, 121.850, 89.339
Angle α, β, γ (deg.)90.00, 94.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ACTIN /


Mass: 41755.617 Da / Num. of mol.: 1 / Fragment: RESIDUES 89-729 / Source method: isolated from a natural source / Source: (natural) SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: G3CKA6
#2: Protein PROTEIN KINASE YOPO


Mass: 71776.875 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA ENTEROCOLITICA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q93KQ6
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 3.4 Å3/Da / Density % sol: 64 % / Description: NONE
Crystal growpH: 7.5 / Details: 30% PEG400, 0.1M HEPES PH7.5, 0.2M SODIUM CHLORIDE

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Details: TOROIDAL FOCUSING MIRROR
RadiationMonochromator: LN2-COOLED, FIXED-EXIT DOUBLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→20 Å / Num. obs: 41770 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.75
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.65 / % possible all: 75.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.4_1496)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3HBT, 2H7O

3hbt

2h7o


Resolution: 2.651→20.022 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 25.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2201 2107 5 %
Rwork0.1856 --
obs0.1873 41765 95.45 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.651→20.022 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7315 0 32 171 7518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027490
X-RAY DIFFRACTIONf_angle_d0.60510142
X-RAY DIFFRACTIONf_dihedral_angle_d12.9172793
X-RAY DIFFRACTIONf_chiral_restr0.0231145
X-RAY DIFFRACTIONf_plane_restr0.0031301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6508-2.71230.28621180.25441931X-RAY DIFFRACTION71
2.7123-2.780.30231170.24952262X-RAY DIFFRACTION82
2.78-2.85490.32241310.25452420X-RAY DIFFRACTION88
2.8549-2.93870.32441240.25722619X-RAY DIFFRACTION94
2.9387-3.03320.29661320.2352731X-RAY DIFFRACTION99
3.0332-3.14120.2911490.23262769X-RAY DIFFRACTION100
3.1412-3.26650.24251370.2192752X-RAY DIFFRACTION100
3.2665-3.41450.24721480.2152765X-RAY DIFFRACTION100
3.4145-3.59350.22161530.19132761X-RAY DIFFRACTION100
3.5935-3.81720.20491380.18122763X-RAY DIFFRACTION100
3.8172-4.10960.20841420.15722773X-RAY DIFFRACTION100
4.1096-4.51880.17131440.14332765X-RAY DIFFRACTION100
4.5188-5.16290.17851620.15172767X-RAY DIFFRACTION100
5.1629-6.46810.21211540.18292781X-RAY DIFFRACTION100
6.4681-20.0230.16841580.14662799X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 41.406 Å / Origin y: 26.8596 Å / Origin z: 12.1554 Å
111213212223313233
T0.1993 Å2-0.0061 Å2-0.0147 Å2-0.1932 Å2-0.0241 Å2--0.2136 Å2
L0.2312 °20 °20.0464 °2-0.8529 °2-0.1863 °2--0.4696 °2
S0.0249 Å °-0.0258 Å °0 Å °-0.0217 Å °-0.0027 Å °0.0321 Å °0.0639 Å °0.0111 Å °-0.0153 Å °
Refinement TLS groupSelection details: ALL

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