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- PDB-1wn9: Crystal structure of the hypothetical protein TT1805 from Thermus... -

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Basic information

Entry
Database: PDB / ID: 1wn9
TitleCrystal structure of the hypothetical protein TT1805 from Thermus thermophillus HB8
Componentsthe hypothetical protein (TT1805)
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Thermus thermophillus / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyTTHA1528-like / hypothetical protein tt1805 / Domain of unknown function DUF3197 / TTHA1528-like superfamily / Protein of unknown function (DUF3197) / 3-Layer(aba) Sandwich / Alpha Beta / ACETIC ACID / Uncharacterized protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.58 Å
AuthorsPioszak, A.A. / Kishishita, S. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of the hypothetical protein TT1805 from Thermus thermophillus HB8
Authors: Pioszak, A.A. / Kishishita, S. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S.
History
DepositionJul 28, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: the hypothetical protein (TT1805)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5093
Polymers14,3891
Non-polymers1202
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.661, 53.997, 36.201
Angle α, β, γ (deg.)90.00, 113.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein the hypothetical protein (TT1805)


Mass: 14389.194 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SI52
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.44 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 14% PEG 8000, 0.1M NaCacodylate, 170mM ZnAcetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Type: SPRING-8 BEAMLINE / Wavelength: 0.979141, 0.979502, 0.964
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: May 24, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791411
20.9795021
30.9641
ReflectionResolution: 1.58→34.12 Å / Num. obs: 34154 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.54722 % / Biso Wilson estimate: 18.6 Å2 / Rsym value: 0.063 / Net I/σ(I): 14.0589
Reflection shellResolution: 1.58→1.64 Å / Mean I/σ(I) obs: 7.37896 / Rsym value: 0.15 / % possible all: 95.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.58→34.12 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1130302.12 / 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
Rfree0.246 1689 5 %RANDOM
Rwork0.214 ---
obs0.214 33802 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.9871 Å2 / ksol: 0.396514 e/Å3
Displacement parametersBiso mean: 19.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20.91 Å2
2---0.42 Å20 Å2
3---0.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.03 Å
Refinement stepCycle: LAST / Resolution: 1.58→34.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms967 0 8 104 1079
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scbond_it2.832
X-RAY DIFFRACTIONc_scangle_it3.722.5
LS refinement shellResolution: 1.58→1.64 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.291 153 4.9 %
Rwork0.223 2972 -
obs--87.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ACETATE.PARMACETATE.TOP

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