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- PDB-3w3d: Crystal structure of smooth muscle G actin DNase I complex -

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Basic information

Entry
Database: PDB / ID: 3w3d
TitleCrystal structure of smooth muscle G actin DNase I complex
Components
  • Actin, gamma-enteric smooth muscle
  • Deoxyribonuclease-1
KeywordsSTRUCTURAL PROTEIN / smooth muscle actin / actin / DNase I / G-actin / ATP Binding
Function / homology
Function and homology information


regulation of neutrophil mediated cytotoxicity / zymogen granule / regulation of acute inflammatory response / deoxyribonuclease I / dynactin complex / deoxyribonuclease I activity / neutrophil activation involved in immune response / DNA catabolic process / actin cytoskeleton / nuclear envelope ...regulation of neutrophil mediated cytotoxicity / zymogen granule / regulation of acute inflammatory response / deoxyribonuclease I / dynactin complex / deoxyribonuclease I activity / neutrophil activation involved in immune response / DNA catabolic process / actin cytoskeleton / nuclear envelope / actin binding / apoptotic process / DNA binding / extracellular region / ATP binding / nucleus / cytoplasm
Similarity search - Function
Deoxyribonuclease I / Deoxyribonuclease I, active site / Deoxyribonuclease I, conservied site / Deoxyribonuclease I signature 2. / Deoxyribonuclease I signature 1. / deoxyribonuclease I / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase ...Deoxyribonuclease I / Deoxyribonuclease I, active site / Deoxyribonuclease I, conservied site / Deoxyribonuclease I signature 2. / Deoxyribonuclease I signature 1. / deoxyribonuclease I / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 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 / 4-Layer Sandwich / Nucleotidyltransferase; domain 5 / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Deoxyribonuclease-1 / Actin, gamma-enteric smooth muscle
Similarity search - Component
Biological speciesGallus gallus (chicken)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsSakabe, N. / Sakabe, K. / Sasaki, K. / Kondo, H. / Shimomur, M.
Citation
Journal: Acta Crystallogr.,Sect.A / Year: 1993
Title: Refined structure and solvent network of chicken gizzard G-actin DNase 1 complex at 1.8A resolution
Authors: Sasaki, K. / Sakabe, K. / Sakabe, N. / Kondo, H. / Shimomur, M.
#1: Journal: Nucl Instrum Methods Phys Res A / Year: 1991
Title: X-ray diffraction data collection system for modern protein crystallography with a Weissenberg camera and an imaging plate using synchrotron radiation
Authors: Sakabe, N.
#2: Journal: J.Biochem. / Year: 1984
Title: X-ray diffraction photographs of chicken gizzard G-actin.DNase I complex crystals taken with synchrotron radiation.
Authors: Sakabe, N. / Kamiya, N. / Sakabe, K. / Kondo, H.
#3: Journal: J.Appl.Crystallogr. / Year: 1983
Title: A F ocusing Weissenberg Camera with Multi-Layer-Line Screens for Macromolecular C rystallography
Authors: Sakabe, N.
#4: Journal: J.Biochem. / Year: 1983
Title: Crystallographic studies of the chicken gizzard G-actin X DNase I complex at 5A resolution
Authors: Sakabe, N. / Sakabe, K. / Sasaki, K. / Kondo, H. / Ema, T. / Kamiya, N. / Matsushima, M.
#5: Journal: J.Biochem. / Year: 1979
Title: Crystallization and preliminary crystallographic data of chicken gizzard G-actin . DNase I complex and Physarum G-actin . DNase I complex
Authors: Sugino, H. / Sakabe, N. / Sakabe, K. / Hatano, S. / Oosawa, F. / Mikawa, T. / Ebashi, S.
#6: Journal: Febs Lett. / Year: 1979
Title: The amino acid sequence of actin from chicken skeletal muscle actin and chicken gizzard smooth muscle actin
Authors: Vandekerckhove, J. / Weber, K.
History
DepositionDec 20, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_label_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin, gamma-enteric smooth muscle
B: Deoxyribonuclease-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6486
Polymers70,8252
Non-polymers1,8224
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-19 kcal/mol
Surface area26870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.000, 225.300, 77.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Actin, gamma-enteric smooth muscle / / Alpha-actin-3 / Gamma-2-actin / Smooth muscle gamma-actin


Mass: 41732.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gizzard / Source: (natural) Gallus gallus (chicken) / References: UniProt: P63270
#2: Protein Deoxyribonuclease-1 / / Deoxyribonuclease I / DNase I


Mass: 29092.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: pancreas / Source: (natural) Bos taurus (cattle) / References: UniProt: P00639, deoxyribonuclease I

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Sugars , 1 types, 1 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-3)-alpha-D- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-3[DManpb1-3DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-2-3-3-2/a4-b1_b4-c1_c3-d1_c6-f1_d6-e1_f3-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][b-D-Manp]{}}}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 386 molecules

#4: 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
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 5

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.42 %
Crystal growTemperature: 300 K / Method: precipitation / pH: 6.6
Details: 4mM MgCl2, 0.1mM CaCl2, NaN3, PEG 6000, pH 6.6, precipitation , temperature 300K

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: Macromolecular data collection system with a Weissenberg camera
Detector: IMAGE PLATE / Date: Feb 15, 1991
Details: The vertically focusing1m long bent mirror of fused silica is 11.5m from the SR source point and 4.6m from the focus point
RadiationMonochromator: A bent triangularly and asymmetrically cut Si(111) crystal is used to focus the beam horizontally and produces monochromatic beams
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Num. obs: 53428 / Biso Wilson estimate: 23.05 Å2

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Processing

Software
NameClassification
WEISdata scaling
BSSdata collection
X-PLORrefinement
WEISdata reduction
RefinementMethod to determine structure: MIR / Resolution: 1.8→10 Å /
RfactorNum. reflection
Rwork0.196 -
obs-53428
Displacement parametersBiso mean: 31.09 Å2
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4973 0 116 383 5472
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.016
X-RAY DIFFRACTIONr_angle_refined_deg3.34

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