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- PDB-2fsk: Crystal structure of Ta0583, an archaeal actin homolog, SeMet data -

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Basic information

Entry
Database: PDB / ID: 2fsk
TitleCrystal structure of Ta0583, an archaeal actin homolog, SeMet data
Componentshypothetical protein Ta0583
KeywordsSTRUCTURAL PROTEIN / Actin homolog / archaea / ATPase / MreB / ParM
Function / homology
Function and homology information


: / Archaeal actin homologue MreB-like, C-terminal / Actin-like protein, N-terminal / Actin like proteins N terminal domain / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Archaeal actin homolog
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsRoeben, A. / Kofler, C. / Nagy, I. / Nickell, S. / Ulrich Hartl, F. / Bracher, A.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal structure of an archaeal actin homolog
Authors: Roeben, A. / Kofler, C. / Nagy, I. / Nickell, S. / Ulrich Hartl, F. / Bracher, A.
History
DepositionJan 23, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein Ta0583
B: hypothetical protein Ta0583


Theoretical massNumber of molelcules
Total (without water)74,8252
Polymers74,8252
Non-polymers00
Water6,828379
1
A: hypothetical protein Ta0583


Theoretical massNumber of molelcules
Total (without water)37,4121
Polymers37,4121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein Ta0583


Theoretical massNumber of molelcules
Total (without water)37,4121
Polymers37,4121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.482, 104.321, 62.546
Angle α, β, γ (deg.)90.00, 96.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein hypothetical protein Ta0583


Mass: 37412.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Strain: DSM 1728 / Gene: Ta0583 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Bl21 / References: UniProt: Q9HKL4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM Bis-Tris pH 6.5, 9-17% PEG-2000MME, 21-22% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9788 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 28, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionRedundancy: 3.7 % / Av σ(I) over netI: 6.4 / Number: 149314 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / D res high: 2.1 Å / D res low: 104.321 Å / Num. obs: 39827 / % possible obs: 100
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)Rmerge(I) obsRsym valueRedundancy
6.6439.96130099.60.0350.0353.7
4.76.6423311000.0430.0433.7
3.834.729911000.0540.0543.8
3.323.8335381000.0620.0623.8
2.973.3239891000.080.083.8
2.712.9744281000.1010.1013.8
2.512.7148141000.1410.1413.8
2.352.5151711000.1870.1873.7
2.212.3554781000.250.253.7
2.12.2157871000.3380.3383.7
ReflectionResolution: 2.1→104.321 Å / Num. obs: 39827 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 26.28 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 6.4
Reflection shellResolution: 2.1→2.21 Å / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 2.1 / Num. measured all: 21583 / Num. unique obs: 5787 / Rsym value: 0.338

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.1 Å / D res low: 20 Å / FOM : 0.19 / Reflection: 39759
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1ANO118.6020.3060.50.1190.824
2ANO132.1210.8880.1230.2150.844
3ANO127.1670.3380.20.2360.802
4ANO119.8140.0490.3960.2090.775
5ANO123.4320.0650.0930.1760.849
6ANO131.2250.4920.4730.170.873
7ANO140.3730.6230.7650.2810.476
8ANO1600.9450.8540.0120.831
9ANO1600.7240.8130.3510.766
10ANO1600.2730.2180.0050.727
11ANO1600.3570.2430.9930.464
Phasing MAD shell
Resolution (Å)FOM Reflection
7.31-200.451968
4.7-7.310.363273
3.7-4.70.284195
3.15-3.70.244910
2.79-3.150.25559
2.52-2.790.146093
2.33-2.520.16643
2.17-2.330.077118
Phasing dmFOM : 0.48 / FOM acentric: 0.48 / FOM centric: 0.45 / Reflection: 39759 / Reflection acentric: 38590 / Reflection centric: 1169
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6-19.9820.880.890.7617041575129
3.8-60.860.860.7253245097227
3-3.80.740.740.6166626455207
2.6-30.510.510.3867296550179
2.3-2.60.290.290.221193011656274
2.1-2.30.150.150.174107257153

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
SOLVE2.01phasing
RESOLVE2.01phasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→62.02 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.696 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1997 5 %RANDOM
Rwork0.174 ---
all0.176 ---
obs-39759 99.86 %-
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: 28.658 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å20.65 Å2
2--0.17 Å20 Å2
3---0.78 Å2
Refinement stepCycle: LAST / Resolution: 2.1→62.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4792 0 0 379 5171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224869
X-RAY DIFFRACTIONr_bond_other_d0.0020.024629
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.9776609
X-RAY DIFFRACTIONr_angle_other_deg0.88310721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4645641
X-RAY DIFFRACTIONr_chiral_restr0.0960.2775
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025462
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02919
X-RAY DIFFRACTIONr_nbd_refined0.2150.2931
X-RAY DIFFRACTIONr_nbd_other0.2450.25370
X-RAY DIFFRACTIONr_nbtor_other0.0860.23079
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2210.2243
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.290.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2930.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.211
X-RAY DIFFRACTIONr_mcbond_it0.9961.53176
X-RAY DIFFRACTIONr_mcangle_it1.86725099
X-RAY DIFFRACTIONr_scbond_it3.06231693
X-RAY DIFFRACTIONr_scangle_it5.1984.51510
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.275 141
Rwork0.2 2786
obs-2927

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