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- PDB-2yxy: Crystarl structure of Hypothetical conserved protein, GK0453 -

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Basic information

Entry
Database: PDB / ID: 2yxy
TitleCrystarl structure of Hypothetical conserved protein, GK0453
ComponentsHypothetical conserved protein, GK0453
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / GK0453 / alpha and beta proteins (a+b) class / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Hypothetical protein YfhH domain / Hypothetical protein YfhH like domains / YfhH-like / Hypothetical protein YfhH / Protein of unknown function (DUF1811) / SH3 type barrels. / Helix Hairpins / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Hypothetical conserved protein
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNakamu, Y. / Bessho, Y. / Padmanabhan, B. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structure of the hypothetical DUF1811-family protein GK0453 from Geobacillus kaustophilus HTA426
Authors: Padmanabhan, B. / Nakamura, Y. / Antonyuk, S.V. / Strange, R.W. / Hasnain, S.S. / Yokoyama, S. / Bessho, Y.
History
DepositionApr 27, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Apr 17, 2013Group: Database references
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical conserved protein, GK0453


Theoretical massNumber of molelcules
Total (without water)13,3031
Polymers13,3031
Non-polymers00
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.689, 75.689, 64.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Hypothetical conserved protein, GK0453


Mass: 13303.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Plasmid: pET-HisTEV / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q5L2U2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 3.45 Å3/Da / Density % sol: 64.4 %
Crystal growTemperature: 293 K / Method: oil-batch / pH: 8.13
Details: 0.1M Tris-HCl, 13.3%(w/v) PEG MME2000, 0.01M NiCl, pH 8.13, oil-batch, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.117 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationMonochromator: double crystal monochromator with sagittal focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.117 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 9975 / Num. obs: 9952 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Redundancy: 10.3 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.078
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.279 / Num. unique all: 957 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345dtbdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SF9

1sf9


Resolution: 2.2→19.95 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 190439.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1015 10.5 %RANDOM
Rwork0.226 ---
obs0.226 9710 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 132.957 Å2 / ksol: 0.524993 e/Å3
Displacement parametersBiso mean: 43.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å20 Å2
2---1.45 Å20 Å2
3---2.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms851 0 0 170 1021
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
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: 2.2→2.34 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 153 10.2 %
Rwork0.225 1353 -
obs--94 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top

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