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- PDB-3eli: Crystal structure of the AHSA1 (SPO3351) protein from Silicibacte... -

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Basic information

Entry
Database: PDB / ID: 3eli
TitleCrystal structure of the AHSA1 (SPO3351) protein from Silicibacter pomeroyi, Northeast Structural Genomics Consortium Target SiR160
ComponentsAha1 domain protein
Keywordsstructural genomics / unknown function / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyActivator of Hsp90 ATPase homologue 1-like / Activator of Hsp90 ATPase homolog 1-like protein / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / Aha1 domain protein
Function and homology information
Biological speciesSilicibacter pomeroyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsForouhar, F. / Su, M. / Seetharaman, J. / Janjua, H. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Wang, D. / Tong, S. / Everett, J.K. ...Forouhar, F. / Su, M. / Seetharaman, J. / Janjua, H. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Wang, D. / Tong, S. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the AHSA1 (SPO3351) protein from Silicibacter pomeroyi, Northeast Structural Genomics Consortium Target SiR160
Authors: Forouhar, F. / Su, M. / Seetharaman, J. / Janjua, H. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Wang, D. / Tong, S. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionSep 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aha1 domain protein


Theoretical massNumber of molelcules
Total (without water)17,5851
Polymers17,5851
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.348, 73.348, 91.891
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Aha1 domain protein / AHSA1


Mass: 17585.045 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter pomeroyi (bacteria) / Strain: DSS-3 / Gene: SPO3351 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q5LN61
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.51 Å3/Da / Density % sol: 65 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 100 mM TAPS (pH 9) and 8.64 M potassium acetate. VAPOR DIFFUSION, HANGING DROP.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97845 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 19, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97845 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 11787 / Num. obs: 11776 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Biso Wilson estimate: 53 Å2 / Rmerge(I) obs: 0.147 / Rsym value: 0.117 / Net I/σ(I): 21.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1164 / Rsym value: 0.368 / % possible all: 99.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXthen SOLVE/RESOLVEmodel building
CNS1.2 & XtalViewrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXthen SOLVE/RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→19.86 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 192372.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 484 5.2 %RANDOM
Rwork0.217 ---
all0.218 11756 --
obs0.217 9335 79.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.6233 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 63.6 Å2
Baniso -1Baniso -2Baniso -3
1-15.48 Å20 Å20 Å2
2--15.48 Å20 Å2
3----30.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1156 0 0 10 1166
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_improper_angle_d1
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.066 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.353 29 6.1 %
Rwork0.277 443 -
obs-443 40.3 %

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