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- PDB-1qz5: Structure of rabbit actin in complex with kabiramide C -

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Basic information

Entry
Database: PDB / ID: 1qz5
TitleStructure of rabbit actin in complex with kabiramide C
ComponentsActin, alpha skeletal muscle
KeywordsSTRUCTURAL PROTEIN / actin / trisoxazole / toxin / kabiramide C
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 / KABIRAMIDE C / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsKlenchin, V.A. / Allingham, J.S. / King, R. / Tanaka, J. / Marriott, G. / Rayment, I.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Trisoxazole macrolide toxins mimic the binding of actin-capping proteins to actin
Authors: Klenchin, V.A. / Allingham, J.S. / King, R. / Tanaka, J. / Marriott, G. / Rayment, I.
History
DepositionSep 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3694
Polymers41,8761
Non-polymers1,4933
Water6,431357
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.919, 70.617, 75.130
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 Actin, alpha skeletal muscle / / Alpha-actin 1


Mass: 41875.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#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-KAB / KABIRAMIDE C


Mass: 946.134 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C48H75N5O14
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.21 Å3/Da / Density % sol: 44.43 %
Crystal growTemperature: 293 K / Method: batch / pH: 5.5
Details: Crystals of the actin-kabiramide C complex were grown by small-scale batch by mixing equal volumes of the complex and 100 mM MES, 18% (w/v) polyethylene glycol 1500, 12% (w/v) 1,6- ...Details: Crystals of the actin-kabiramide C complex were grown by small-scale batch by mixing equal volumes of the complex and 100 mM MES, 18% (w/v) polyethylene glycol 1500, 12% (w/v) 1,6-hexanediol, 100 mM CaCl2, 1 mM sodium azide, 1 mM TCEP, pH 5.5, Batch, temperature 293K
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110-12 mg/mlprotein11
2100 mMMES11pH5.5
318 %(w/v)PEG150011
412 %(w/v)1,6-hexanediol11
5100 mM11CaCl2
61 mM11NaN3
71 mMTCEP11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 23, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.45→54 Å / Num. all: 65708 / Num. obs: 65708 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 47.1
Reflection shellResolution: 1.45→1.5 Å / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 13.9 / Num. unique all: 6310 / % possible all: 10
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 542898
Reflection shell
*PLUS
% possible obs: 95.7 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.984 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.067 / ESU R Free: 0.065 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18691 5129 7.8 %RANDOM
Rwork0.16855 ---
obs0.17001 60570 98.42 %-
all-61542 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.301 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2---0.23 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2843 0 99 357 3299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213008
X-RAY DIFFRACTIONr_bond_other_d0.0020.022735
X-RAY DIFFRACTIONr_angle_refined_deg1.6692.0014088
X-RAY DIFFRACTIONr_angle_other_deg1.636398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5855359
X-RAY DIFFRACTIONr_chiral_restr0.2010.2467
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023245
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02566
X-RAY DIFFRACTIONr_nbd_refined0.2150.2597
X-RAY DIFFRACTIONr_nbd_other0.2410.23335
X-RAY DIFFRACTIONr_nbtor_other0.090.21723
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2480.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4820.229
X-RAY DIFFRACTIONr_mcbond_it0.9261.51799
X-RAY DIFFRACTIONr_mcangle_it1.6922926
X-RAY DIFFRACTIONr_scbond_it2.4531209
X-RAY DIFFRACTIONr_scangle_it3.7824.51162
LS refinement shellResolution: 1.45→1.5 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.223 328
Rwork0.188 4221
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.188 / Rfactor Rwork: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.67
LS refinement shell
*PLUS
Rfactor Rwork: 0.187

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