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- PDB-2gwj: SpvB ADP-ribosylated actin: hexagonal crystal form -

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Basic information

Entry
Database: PDB / ID: 2gwj
TitleSpvB ADP-ribosylated actin: hexagonal crystal form
ComponentsActin, alpha skeletal muscle
KeywordsCONTRACTILE PROTEIN / actin / ADP-ribosylation
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 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsStebbins, C.E. / Margarit, S.M.
CitationJournal: Structure / Year: 2006
Title: A steric antagonism of actin polymerization by a salmonella virulence protein.
Authors: Margarit, S.M. / Davidson, W. / Frego, L. / Stebbins, C.E.
History
DepositionMay 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9343
Polymers41,3871
Non-polymers5472
Water7,512417
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.361, 96.361, 97.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 41387.227 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 3.15 Å3/Da / Density % sol: 61 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979 Å
DetectorDate: Oct 19, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→99 Å / Num. obs: 57844 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.051 / Χ2: 1.044 / Net I/σ(I): 14.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.765.60.72857081.0151100
1.76-1.835.60.525574611100
1.83-1.915.60.41156941.0861100
1.91-2.025.60.24457481.0661100
2.02-2.145.60.16457531.0781100
2.14-2.315.60.11657351.0941100
2.31-2.546.50.08457941.0141100
2.54-2.9111.20.08157871.0311100
2.91-3.6611.20.04358361.0541100
3.66-9910.80.02560431.027199.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→83.33 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.901 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.184 2041 5.1 %RANDOM
Rwork0.152 ---
all0.153 ---
obs0.153 39922 95.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.119 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20.41 Å20 Å2
2--0.82 Å20 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 1.9→83.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2821 0 32 417 3270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222914
X-RAY DIFFRACTIONr_bond_other_d0.0020.022635
X-RAY DIFFRACTIONr_angle_refined_deg1.8691.9843955
X-RAY DIFFRACTIONr_angle_other_deg1.27936138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7725356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3223.952124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15915496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0591518
X-RAY DIFFRACTIONr_chiral_restr0.1420.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023187
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02575
X-RAY DIFFRACTIONr_nbd_refined0.2490.2657
X-RAY DIFFRACTIONr_nbd_other0.2120.22790
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21427
X-RAY DIFFRACTIONr_nbtor_other0.0930.21629
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.2315
X-RAY DIFFRACTIONr_metal_ion_refined0.0810.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.310.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.223
X-RAY DIFFRACTIONr_mcbond_it1.2691.51846
X-RAY DIFFRACTIONr_mcbond_other0.3631.5732
X-RAY DIFFRACTIONr_mcangle_it1.84622900
X-RAY DIFFRACTIONr_scbond_it3.38631233
X-RAY DIFFRACTIONr_scangle_it4.9634.51055
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 115 -
Rwork0.157 2511 -
obs-2626 86.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.66240.2438-0.10530.7568-0.33252.03280.06030.09170.16630.0159-0.0386-0.1045-0.30090.2081-0.0218-0.0028-0.04090.0258-0.16370.0054-0.084554.30116.57541.448
22.15210.40510.36041.31960.3652.01210.063-0.1393-0.12440.1443-0.0327-0.14760.01710.1442-0.0304-0.011-0.02940.0042-0.17780.0117-0.109452.2047.10653.267
32.42920.5145-1.51443.5234-2.07517.30310.0128-0.1709-0.25520.1577-0.0781-0.11010.5145-0.0190.0652-0.0142-0.0427-0.0115-0.1749-0.0068-0.098140.02-3.07445.959
42.88840.79440.72181.86580.94424.5708-0.10620.27790.3376-0.26840.03420.1758-0.6133-0.17530.0720.05180.0149-0.0091-0.070.0343-0.077433.32710.48722.321
51.05360.10410.73211.0644-0.10383.81990.1023-0.0893-0.08060.0367-0.00970.13390.4156-0.4551-0.0926-0.0191-0.06990.013-0.0570.0068-0.064431.087-3.67440.788
64.6304-2.39752.8881.6869-1.17232.1148-0.0255-0.5885-0.17790.3880.09790.0033-0.0888-0.1147-0.07240.0589-0.04390.0132-0.06160.0252-0.058850.1777.91560.802
70.83891.10861.36652.34430.50234.1584-0.1260.00930.1793-0.11450.01330.0373-0.1753-0.31850.1127-0.06530.00480.0243-0.15590.0073-0.142740.46310.49636.417
81.57510.48540.70560.91710.21172.0680.00160.04140.0342-0.02180.00790.0106-0.0422-0.0965-0.00960.08680.01010.0347-0.04880.00070.020842.1846.36838.907
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 99
2X-RAY DIFFRACTION2A100 - 146
3X-RAY DIFFRACTION3A147 - 181
4X-RAY DIFFRACTION4A182 - 261
5X-RAY DIFFRACTION5A262 - 338
6X-RAY DIFFRACTION6A339 - 375
7X-RAY DIFFRACTION7A1380
8X-RAY DIFFRACTION8A1402 - 1818

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