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- PDB-3qoo: Crystal structure of hot-dog-like Taci_0573 protein from Thermana... -

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Basic information

Entry
Database: PDB / ID: 3qoo
TitleCrystal structure of hot-dog-like Taci_0573 protein from Thermanaerovibrio acidaminovorans
ComponentsUncharacterized protein
KeywordsStructural genomics / Unknown function / PSI-Biology / Midwest Center for Structural Genomics / MCSG / hot-dog superfamily
Function / homologyFluoroacetyl-CoA thioesterase / : / Fluoroacetyl-CoA-specific thioesterase / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / Fluoroacetyl-CoA-specific thioesterase-like domain-containing protein
Function and homology information
Biological speciesThermanaerovibrio acidaminovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.25 Å
AuthorsMichalska, K. / Li, H. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of hot-dog-like Taci_0573 protein from Thermanaerovibrio acidaminovorans
Authors: Michalska, K. / Li, H. / Clancy, S. / Joachimiak, A.
History
DepositionFeb 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 27, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6846
Polymers15,5191
Non-polymers1655
Water1,910106
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,36712
Polymers31,0382
Non-polymers33010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area5260 Å2
ΔGint-106 kcal/mol
Surface area12690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.078, 38.078, 142.148
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein Uncharacterized protein


Mass: 15518.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermanaerovibrio acidaminovorans (bacteria)
Strain: DSM 6589 / Gene: Taci_0573 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: D1B956
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 1.92 Å3/Da / Density % sol: 35.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M MgCl2, 0.1 M sodium citrate, 40% PEG400, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791829 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2010 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791829 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. all: 34231 / Num. obs: 34179 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 23.6
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 2.1 / % possible all: 98.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
Cootmodel building
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.25→47.38 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.384 / SU ML: 0.028 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. There is a strong positive peak in Fo-Fc electron density map near Lys126 most likely corresponding to a small ligand molecule but we were ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. There is a strong positive peak in Fo-Fc electron density map near Lys126 most likely corresponding to a small ligand molecule but we were unable to unambiguously identify and model it.
RfactorNum. reflection% reflectionSelection details
Rfree0.18051 1070 3.1 %RANDOM
Rwork0.15594 ---
obs0.1567 32906 99.45 %-
all-33976 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.416 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0.19 Å20 Å2
2---0.38 Å20 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.25→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1053 0 5 106 1164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221168
X-RAY DIFFRACTIONr_bond_other_d0.0010.02791
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.9581596
X-RAY DIFFRACTIONr_angle_other_deg0.90331925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1035153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.16523.21456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39515205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.951513
X-RAY DIFFRACTIONr_chiral_restr0.0920.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021354
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02250
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6631.5730
X-RAY DIFFRACTIONr_mcbond_other0.4641.5293
X-RAY DIFFRACTIONr_mcangle_it2.67121202
X-RAY DIFFRACTIONr_scbond_it3.5053438
X-RAY DIFFRACTIONr_scangle_it5.24.5394
X-RAY DIFFRACTIONr_rigid_bond_restr1.34531959
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.251→1.284 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 76 -
Rwork0.285 2379 -
obs--98.55 %

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