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- PDB-1wws: Crystal structure of ttk003001566 from Thermus Thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 1wws
TitleCrystal structure of ttk003001566 from Thermus Thermophilus HB8
Componentshypothetical protein TTHA1479
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


protein heterodimerization activity
Similarity search - Function
Protein of unknown function DUF1931 / Domain of unknown function (DUF1931) / Histone, subunit A / Histone, subunit A / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DUF1931 family protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWang, H. / Murayama, K. / Terada, T. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: to be published
Title: Crystal structure of ttk003001566 from Thermus Thermophilus HB8
Authors: Wang, H. / Murayama, K. / Terada, T. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S.
History
DepositionJan 18, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 20, 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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: hypothetical protein TTHA1479
B: hypothetical protein TTHA1479
C: hypothetical protein TTHA1479
D: hypothetical protein TTHA1479
E: hypothetical protein TTHA1479
F: hypothetical protein TTHA1479
G: hypothetical protein TTHA1479
H: hypothetical protein TTHA1479
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,42614
Polymers136,1868
Non-polymers2406
Water12,773709
1
A: hypothetical protein TTHA1479
B: hypothetical protein TTHA1479
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1274
Polymers34,0462
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-22 kcal/mol
Surface area13310 Å2
MethodPISA
2
C: hypothetical protein TTHA1479
D: hypothetical protein TTHA1479
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0873
Polymers34,0462
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-16 kcal/mol
Surface area13080 Å2
MethodPISA
3
E: hypothetical protein TTHA1479
F: hypothetical protein TTHA1479
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1274
Polymers34,0462
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-19 kcal/mol
Surface area13220 Å2
MethodPISA
4
G: hypothetical protein TTHA1479
H: hypothetical protein TTHA1479
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0873
Polymers34,0462
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-18 kcal/mol
Surface area13090 Å2
MethodPISA
5
A: hypothetical protein TTHA1479
B: hypothetical protein TTHA1479
hetero molecules

C: hypothetical protein TTHA1479
D: hypothetical protein TTHA1479
hetero molecules

G: hypothetical protein TTHA1479
H: hypothetical protein TTHA1479
hetero molecules

E: hypothetical protein TTHA1479
F: hypothetical protein TTHA1479
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,42614
Polymers136,1868
Non-polymers2406
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation2_756-x+2,y+1/2,-z+11
crystal symmetry operation2_655-x+1,y+1/2,-z1
Buried area15120 Å2
ΔGint-166 kcal/mol
Surface area49370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.770, 70.580, 97.900
Angle α, β, γ (deg.)90.00, 106.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
hypothetical protein TTHA1479 / ttk003001566


Mass: 17023.221 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: GenBank: 55981448, UniProt: Q5SI95*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 709 / 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: 2.3 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG3350, Calcium Chloride, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Sep 26, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 92901 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 20.7 Å2 / Rsym value: 0.087 / Net I/σ(I): 14.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 8892 / Rsym value: 0.291 / % possible all: 95.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→44 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 573451.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.254 4564 5 %RANDOM
Rwork0.208 ---
obs0.208 90766 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.0423 Å2 / ksol: 0.334622 e/Å3
Displacement parametersBiso mean: 33.2 Å2
Baniso -1Baniso -2Baniso -3
1-7.23 Å20 Å23.67 Å2
2---6.93 Å20 Å2
3----0.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.9→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9504 0 6 709 10219
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 684 4.9 %
Rwork0.264 13396 -
obs--90.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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