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- PDB-3ea0: Crystal Structure of ParA Family ATPase from Chlorobium tepidum TLS -

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Basic information

Entry
Database: PDB / ID: 3ea0
TitleCrystal Structure of ParA Family ATPase from Chlorobium tepidum TLS
ComponentsATPase, ParA family
KeywordsHYDROLASE / alpha-beta-alpha sandwich / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


negative regulation of cell division / cytoplasmic side of plasma membrane / ATP hydrolysis activity / ATP binding / metal ion binding / cytosol
Similarity search - Function
: / AAA domain / AAA domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / ATPase, ParA family
Similarity search - Component
Biological speciesChlorobium tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsKim, Y. / Tesar, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of ParA Family ATPase from Chlorobium tepidum TLS
Authors: Kim, Y. / Tesar, C. / Clancy, S. / Joachimiak, A.
History
DepositionAug 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 6, 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATPase, ParA family
B: ATPase, ParA family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0716
Polymers54,0082
Non-polymers1,0634
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-30 kcal/mol
Surface area19870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.572, 67.032, 134.786
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 ATPase, ParA family


Mass: 27004.229 Da / Num. of mol.: 2 / Fragment: residues 36-277
Source method: isolated from a genetically manipulated source
Details: N-terminal 6 His tag with TEV protease cut site / Source: (gene. exp.) Chlorobium tepidum (bacteria) / Strain: TLS / Gene: CT0433 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q8KF94
#2: Chemical ChemComp-ATP / ADENOSINE-5'-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.12 Å3/Da / Density % sol: 41.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M MgCl2, 0.1M BisTris pH6.5, 25 % PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 21, 2008 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→40.45 Å / Num. obs: 44390 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Biso Wilson estimate: 32.49 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 6.8
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1122 / % possible all: 95.2

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
Cootmodel building
PHENIX(phenix.refine)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→40.45 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MLHL / Details: number of reflections contains both F+ and F-.
RfactorNum. reflection% reflectionSelection details
Rfree0.2516 2279 5.13 %Random
Rwork0.1941 ---
all0.197 44390 --
obs0.197 44390 98.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.308 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso mean: 48.27 Å2
Baniso -1Baniso -2Baniso -3
1-17.391 Å2-0 Å2-0 Å2
2---14.6967 Å20 Å2
3----2.6943 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3722 0 64 112 3898
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_deg1.145
X-RAY DIFFRACTIONf_dihedral_angle_d20.77
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.2-2.24780.28861470.26312398254590
2.2478-2.30010.33461500.26122541269196
2.3001-2.35760.27511420.23772590273298
2.3576-2.42140.26691400.24422672281299
2.4214-2.49260.35751290.23626552784100
2.4926-2.57310.29071450.222826692814100
2.5731-2.6650.27351530.212926812834100
2.665-2.77170.271480.210526452793100
2.7717-2.89780.29311280.209226712799100
2.8978-3.05050.2621430.204826542797100
3.0505-3.24160.28441220.202426902812100
3.2416-3.49170.22971760.179626122788100
3.4917-3.84290.20331460.158426682814100
3.8429-4.39840.23311360.159726772813100
4.3984-5.53920.23411540.167626512805100
5.5392-40.45660.21391200.18392637275798
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.59630.0767-0.09442.328-0.41481.11130.0890.0217-0.01660.08580.07670.09280.16530.0086-0.1710.29450.02360.00860.2009-0.00390.187424.859-13.322850.7381
20.75710.4063-0.18873.5575-0.40931.5825-0.05240.0477-0.02360.08270.1261-0.21790.02650.0681-0.07330.17020.02180.03040.1958-0.05740.187735.614313.178252.0623
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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