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- PDB-2dev: Crystal structure of tt0972 protein from Thermus Thermophilus wit... -

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Basic information

Entry
Database: PDB / ID: 2dev
TitleCrystal structure of tt0972 protein from Thermus Thermophilus with Cs(+) ions
Componentstt0972 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / dodecamer / flavin / cesium ion / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


: / Dodecin / Dodecin-like superfamily / Dodecin / Flavin-binding protein dodecin / Dodecin-like / Dodecin subunit-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.45 Å
AuthorsInagaki, E. / Nakano, N. / Shinkai, A. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of tt0972 protein from Thermus Thermophilus
Authors: Inagaki, E. / Nakano, N. / Shinkai, A. / Yokoyama, S.
History
DepositionFeb 17, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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_conn.ptnr2_label_seq_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: tt0972 protein
B: tt0972 protein
C: tt0972 protein
D: tt0972 protein
E: tt0972 protein
F: tt0972 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,78610
Polymers46,5606
Non-polymers2274
Water82946
1
A: tt0972 protein
B: tt0972 protein
C: tt0972 protein
D: tt0972 protein
E: tt0972 protein
F: tt0972 protein
hetero molecules

A: tt0972 protein
B: tt0972 protein
C: tt0972 protein
D: tt0972 protein
E: tt0972 protein
F: tt0972 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,57320
Polymers93,11912
Non-polymers4548
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
MethodPQS
2
C: tt0972 protein

B: tt0972 protein
E: tt0972 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3154
Polymers23,2803
Non-polymers351
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation8_555-y,-x,-z+1/21
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-13 kcal/mol
Surface area12020 Å2
MethodPISA
3
D: tt0972 protein
hetero molecules

A: tt0972 protein
F: tt0972 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4716
Polymers23,2803
Non-polymers1913
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation8_555-y,-x,-z+1/21
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-22 kcal/mol
Surface area12090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.764, 65.764, 204.285
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a dodecamer generated from the two trimers in the asymmetric unit by the operations: -x, -y, -z+1/2

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Components

#1: Protein
tt0972 protein


Mass: 7759.931 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: GenBank: 55772813, UniProt: Q72IR6*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cs
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.37 Å3/Da / Density % sol: 48.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 6% PEG 4000, 60mM sodium acetate, 60mM lithium chloride, 100mM cesium chloride, 0.5mM nickel chloride, 30mM TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9791 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 28, 2004 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.45→20 Å / Num. all: 17359 / Num. obs: 17151 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 34.9
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1626 / % possible all: 97.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
BSSdata collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2DEH

2deh


Resolution: 2.45→19.89 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 133174.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.288 805 4.8 %RANDOM
Rwork0.246 ---
all0.248 17151 --
obs0.246 16631 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.8633 Å2 / ksol: 0.327525 e/Å3
Displacement parametersBiso mean: 55.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.88 Å20 Å20 Å2
2--2.88 Å20 Å2
3----5.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.45→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 0 4 46 3246
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0.67
LS refinement shellResolution: 2.45→2.6 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.423 118 4.8 %
Rwork0.367 2365 -
obs--89 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramion.top
X-RAY DIFFRACTION3ion.paramwater.top

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