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- PDB-1vgg: Crystal Structure of the Conserved Hypothetical Protein TTHA1091 ... -

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Basic information

Entry
Database: PDB / ID: 1vgg
TitleCrystal Structure of the Conserved Hypothetical Protein TTHA1091 from Thermus Thermophilus HB8
ComponentsConserved Hypothetical Protein TT1634 (TTHA1091)
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Thermus Thermophilus HB8 / Conserved Hypothetical Protein / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyTa1353-like / Adenosine specific kinase / Ta1353-like superfamily / Adenosine specific kinase / hypothetical protein tt1634 / 3-Layer(aba) Sandwich / Alpha Beta / Adenosine monophosphate-protein transferase
Function and homology information
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsSatoh, S. / Yao, M. / Kousumi, Y. / Ebihara, A. / Matsumoto, K. / Okamoto, A. / Tanaka, I. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of the Conserved Hypothetical Protein TT1634 from Thermus Thermophilus HB8
Authors: Satoh, S. / Yao, M. / Kousumi, Y. / Ebihara, A. / Matsumoto, K. / Okamoto, A. / Tanaka, I. / Yokoyama, S. / Kuramitsu, S.
History
DepositionApr 26, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 30, 2014Group: Source and taxonomy / Structure summary
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conserved Hypothetical Protein TT1634 (TTHA1091)
B: Conserved Hypothetical Protein TT1634 (TTHA1091)
C: Conserved Hypothetical Protein TT1634 (TTHA1091)
D: Conserved Hypothetical Protein TT1634 (TTHA1091)
E: Conserved Hypothetical Protein TT1634 (TTHA1091)
F: Conserved Hypothetical Protein TT1634 (TTHA1091)


Theoretical massNumber of molelcules
Total (without water)106,5156
Polymers106,5156
Non-polymers00
Water8,197455
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28040 Å2
ΔGint-103 kcal/mol
Surface area29470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.490, 100.440, 104.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Conserved Hypothetical Protein TT1634 (TTHA1091)


Mass: 17752.438 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: TTHA1091 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SJC3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 2.03 Å3/Da / Density % sol: 38.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: PEG 200, sodium acetate, sodium chloride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9722, 0.9794, 0.9798
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 3, 2003
RadiationMonochromator: SI 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97221
20.97941
30.97981
ReflectionResolution: 1.75→20 Å / Num. all: 90161 / Num. obs: 90161 / % possible obs: 99 % / Redundancy: 5.3 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 27.9
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 5 % / Rmerge(I) obs: 0.134 / Mean I/σ(I) obs: 9.8 / Num. unique all: 8961 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→19.93 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2015553.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: The structure was refined also with Lafire
RfactorNum. reflection% reflectionSelection details
Rfree0.204 8944 10 %RANDOM
Rwork0.18 ---
all0.182 89272 --
obs0.182 89272 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.5628 Å2 / ksol: 0.420015 e/Å3
Displacement parametersBiso mean: 16.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.29 Å20 Å20 Å2
2---0.54 Å20 Å2
3----1.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å-0.04 Å
Refinement stepCycle: LAST / Resolution: 1.75→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7458 0 0 455 7913
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it1.872
X-RAY DIFFRACTIONc_scbond_it2.682
X-RAY DIFFRACTIONc_scangle_it3.762.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.23 1481 10.4 %
Rwork0.186 12728 -
obs--94.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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