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- PDB-2ba2: Crystal structure of the DUF16 domain of MPN010 from Mycoplasma p... -

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Basic information

Entry
Database: PDB / ID: 2ba2
TitleCrystal structure of the DUF16 domain of MPN010 from Mycoplasma pneumoniae
ComponentsHypothetical UPF0134 protein MPN010
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / DUF16 / MPN010 / hypothetical protein / coiled-coil / stutter / PSI / Protein Structure Initiative / Berkeley Structural Genomics Center / BSGC
Function / homologySingle alpha-helices involved in coiled-coils or other helix-helix interfaces - #40 / Domain of unknown function DUF16 / Protein of unknown function DUF16 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / UPF0134 protein MPN_010
Function and homology information
Biological speciesMycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsShin, D.H. / Kim, J.-S. / Yokota, H. / Kim, R. / Kim, S.-H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Protein Sci. / Year: 2006
Title: Crystal structure of the DUF16 domain of MPN010 from Mycoplasma pneumoniae.
Authors: Shin, D.H. / Kim, J.-S. / Yokota, H. / Kim, R. / Kim, S.-H.
History
DepositionOct 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical UPF0134 protein MPN010
B: Hypothetical UPF0134 protein MPN010
C: Hypothetical UPF0134 protein MPN010


Theoretical massNumber of molelcules
Total (without water)29,3673
Polymers29,3673
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9870 Å2
ΔGint-77 kcal/mol
Surface area14600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.559, 38.874, 68.734
Angle α, β, γ (deg.)90.00, 99.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hypothetical UPF0134 protein MPN010 / D12_orf131


Mass: 9789.110 Da / Num. of mol.: 3 / Fragment: DUF16 domain, residues 46-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
Plasmid: pB3, pET21a derived / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3), pSJS1244 / References: UniProt: P75103
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 1.91 Å3/Da / Density % sol: 33.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M lithium Sulfate, 25% PEG3350, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97938 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 11, 2005 / Details: Monochromator
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97938 Å / Relative weight: 1
ReflectionResolution: 1.8→42.01 Å / Num. all: 40349 / Num. obs: 32441 / % possible obs: 80.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.3 Å2
Reflection shellResolution: 1.8→1.83 Å / % possible all: 13

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→19.55 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 215255.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1651 10 %RANDOM
Rwork0.229 ---
all0.234 20869 --
obs0.229 16591 79.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.6333 Å2 / ksol: 0.405914 e/Å3
Displacement parametersBiso mean: 31.1 Å2
Baniso -1Baniso -2Baniso -3
1--5.82 Å20 Å25.04 Å2
2--5.82 Å20 Å2
3---0.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1970 0 0 190 2160
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_dihedral_angle_d15.3
X-RAY DIFFRACTIONc_improper_angle_d0.62
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 58 8 %
Rwork0.268 671 -
obs--21.2 %
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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