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- PDB-6qri: Structure of rabbit G-actin in complex with chivosazole A -

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Basic information

Entry
Database: PDB / ID: 6qri
TitleStructure of rabbit G-actin in complex with chivosazole A
ComponentsActin, alpha skeletal muscle
KeywordsCYTOSOLIC PROTEIN / cytoskeleton / macrolide / myxobacteria
Function / homology
Function and homology information


cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament ...cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / 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; Chain A, domain 2 / Actin; Chain A, domain 2 / 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 / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Chem-CV9 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSchneider, S. / Wang, S. / Zahler, S.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationSCHN1273/6-1 Germany
German Research FoundationSFB1032 Germany
CitationJournal: J.Nat.Prod. / Year: 2019
Title: Chivosazole A Modulates Protein-Protein Interactions of Actin.
Authors: Wang, S. / Gegenfurtner, F.A. / Crevenna, A.H. / Ziegenhain, C. / Kliesmete, Z. / Enard, W. / Muller, R. / Vollmar, A.M. / Schneider, S. / Zahler, S.
History
DepositionFeb 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: 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
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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Actin, alpha skeletal muscle
A: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0158
Polymers84,2202
Non-polymers2,7956
Water82946
1
B: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5084
Polymers42,1101
Non-polymers1,3983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5084
Polymers42,1101
Non-polymers1,3983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.540, 78.619, 77.055
Angle α, β, γ (deg.)90.000, 115.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Actin, alpha skeletal muscle / / Alpha-actin-1


Mass: 42109.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: ACTA1, ACTA / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CV9 / (2~{R},3~{R},5~{S},6~{E},8~{E},10~{Z},12~{S},13~{R},16~{Z},18~{E},20~{Z},22~{E},24~{R},25~{S},26~{E},28~{Z})-13-[(2~{S},3~{S},5~{S})-3,5-bis(oxidanyl)hexan-2-yl]-25-[(2~{R},3~{R},4~{S},5~{R},6~{R})-3,4-dimethoxy-6-methyl-5-oxidanyl-oxan-2-yl]oxy-3-methoxy-2,12,22,24-tetramethyl-5-oxidanyl-14,32-dioxa-33-azabicyclo[28.2.1]tritriaconta-1(33),6,8,10,16,18,20,22,26,28,30-undecaen-15-one


Mass: 866.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H71NO12 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.5 M lithium chloride, 100 mM Tris(hydroxymethyl)aminomethane hydrochloride (Tris-HCl), 28 % (w/v) polyethylenglycol 6000, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.4→49.2 Å / Num. obs: 30437 / % possible obs: 98.8 % / Redundancy: 3.6 % / CC1/2: 0.99 / Net I/σ(I): 7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 0.98 / Num. unique obs: 2925 / CC1/2: 0.47 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YXQ

1yxq


Resolution: 2.4→49.16 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.911 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.599 / ESU R Free: 0.296
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2683 1523 5 %RANDOM
Rwork0.2364 ---
obs0.238 28923 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 143.23 Å2 / Biso mean: 55.698 Å2 / Biso min: 18.03 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å2-0 Å2-0.45 Å2
2--0.18 Å20 Å2
3---1.24 Å2
Refinement stepCycle: final / Resolution: 2.4→49.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5618 0 188 46 5852
Biso mean--50.98 42.01 -
Num. residues----718
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0135942
X-RAY DIFFRACTIONr_bond_other_d0.0350.0175496
X-RAY DIFFRACTIONr_angle_refined_deg1.9471.688069
X-RAY DIFFRACTIONr_angle_other_deg2.3081.60612764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4685716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5522.226283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78415992
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8651536
X-RAY DIFFRACTIONr_chiral_restr0.1160.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026517
X-RAY DIFFRACTIONr_gen_planes_other0.0140.021241
X-RAY DIFFRACTIONr_mcbond_it1.7925.9422870
X-RAY DIFFRACTIONr_mcbond_other1.795.9422869
X-RAY DIFFRACTIONr_mcangle_it3.0978.9093581
LS refinement shellResolution: 2.398→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 102 -
Rwork0.375 1928 -
all-2030 -
obs--89.98 %

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