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- PDB-3vqj: Crystal Structutre of Thiobacillus thioparus THI115 Carbonyl Sulf... -

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Basic information

Entry
Database: PDB / ID: 3vqj
TitleCrystal Structutre of Thiobacillus thioparus THI115 Carbonyl Sulfide Hydrolase
ComponentsCarbonyl sulfide hydrolase
KeywordsHYDROLASE / ALPHA/BETA-FOLD / homotetramer
Function / homology
Function and homology information


carbonyl sulfide hydrolase / carbonate dehydratase activity / hydrolase activity / zinc ion binding
Similarity search - Function
Beta-carbonic Anhydrase; Chain A / Carbonic anhydrase / Carbonic anhydrase / Carbonic anhydrase superfamily / Carbonic anhydrase / Carbonic anhydrase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Carbonyl sulfide hydrolase
Similarity search - Component
Biological speciesThiobacillus thioparus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsKatayama, Y. / Noguchi, K. / Ogawa, T. / Ohtaki, A. / Odaka, M. / Yohda, M.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Carbonyl Sulfide Hydrolase from Thiobacillus thioparus Strain THI115 Is One of the beta-Carbonic Anhydrase Family Enzymes
Authors: Ogawa, T. / Noguchi, K. / Saito, M. / Nagahata, Y. / Kato, H. / Ohtaki, A. / Nakayama, H. / Dohmae, N. / Matsushita, Y. / Odaka, M. / Yohda, M. / Nyunoya, H. / Katayama, Y.
History
DepositionMar 24, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_alt_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_alt_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_ptnr2_label_alt_id / _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_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: Carbonyl sulfide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4713
Polymers23,3821
Non-polymers882
Water4,612256
1
A: Carbonyl sulfide hydrolase
hetero molecules

A: Carbonyl sulfide hydrolase
hetero molecules

A: Carbonyl sulfide hydrolase
hetero molecules

A: Carbonyl sulfide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,88412
Polymers93,5304
Non-polymers3548
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation15_544y+1/2,x-1/2,-z-1/21
crystal symmetry operation16_444-y-1/2,-x-1/2,-z-1/21
Buried area18480 Å2
ΔGint-294 kcal/mol
Surface area25710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.239, 90.239, 104.976
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-302-

NA

21A-417-

HOH

31A-528-

HOH

41A-543-

HOH

51A-648-

HOH

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Components

#1: Protein Carbonyl sulfide hydrolase


Mass: 23382.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thiobacillus thioparus (bacteria) / Strain: THI115 / Gene: cos / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: H1AAP2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.28 Å3/Da / Density % sol: 46.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.2M AMMONIUM SULFATE, 200mM SODIIUM CHLORIDE, 30% GLYCEROL, 100mM TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Oct 30, 2009
RadiationMonochromator: Triangular Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. all: 67414 / Num. obs: 67414 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 7.4 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 35.6
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 7.6 / Num. unique all: 6662 / Rsym value: 0.315 / % possible all: 100

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Processing

Software
NameClassification
SERGUIdata collection
MOLREPphasing
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YLK

1ylk


Resolution: 1.2→10 Å / Num. parameters: 16405 / Num. restraintsaints: 18243 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1698 3373 -RANDOM
Rwork0.1353 ---
obs0.1353 63916 94.8 %-
all-63916 --
Displacement parametersBiso mean: 4.1 Å2
Refine analyzeNum. disordered residues: 21 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1835.8
Refinement stepCycle: LAST / Resolution: 1.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1587 0 2 256 1845
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0308
X-RAY DIFFRACTIONs_zero_chiral_vol0.076
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.085
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.023
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.025
X-RAY DIFFRACTIONs_approx_iso_adps0.052

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