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- PDB-3hlu: Crystal Structure of Uncharacterized Protein Conserved in Bacteri... -

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Basic information

Entry
Database: PDB / ID: 3hlu
TitleCrystal Structure of Uncharacterized Protein Conserved in Bacteria DUF2179 from Eubacterium ventriosum
Componentsuncharacterized protein DUF2179
Keywordsstructural genomics / unknown function / alpha-beta half sandwich / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Uncharacterised membrane protein YitT / Domain of unknown function DUF2179 / : / Uncharacterised 5xTM membrane BCR, YitT family COG1284 / Uncharacterized protein conserved in bacteria (DUF2179) / Alpha-Beta Plaits - #120 / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DUF2179 domain-containing protein
Similarity search - Component
Biological speciesEubacterium ventriosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsKim, Y. / Li, H. / Keigher, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published / Year: 2009
Title: Crystal Structure of Uncharacterized Protein Conserved in Bacteria DUF2179 from Eubacterium ventriosum
Authors: Kim, Y. / Li, H. / Keigher, L. / Joachimiak, A.
History
DepositionMay 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 6, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized protein DUF2179
B: uncharacterized protein DUF2179


Theoretical massNumber of molelcules
Total (without water)22,1642
Polymers22,1642
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-14 kcal/mol
Surface area8230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.588, 63.392, 82.197
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 uncharacterized protein DUF2179


Mass: 11081.837 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium ventriosum (bacteria) / Strain: ATCC 27560 / Gene: EUBVEN_01903 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 magic / References: UniProt: A5Z863
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.74 Å3/Da / Density % sol: 67.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M NaCl, 0.1 M HEPES pH 7.5, 30% (v/v) PEG-400, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 22, 2009 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.65→50.295 Å / Num. all: 10088 / Num. obs: 10088 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 91.6 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 11.7
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 2.6 / Num. unique all: 466 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
PHENIX(phenix.refine)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.65→41.1034 Å / SU ML: 0.31 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.252 482 4.8 %RANDOM
Rwork0.226 ---
all0.227 10049 --
obs0.227 10049 98.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.805 Å2 / ksol: 0.317 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.714 Å20 Å2-0 Å2
2--9.5757 Å20 Å2
3----16.2897 Å2
Refinement stepCycle: LAST / Resolution: 2.65→41.1034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1148 0 0 26 1174
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_deg1.271
X-RAY DIFFRACTIONf_dihedral_angle_d20.15
X-RAY DIFFRACTIONf_planarity0.004
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.65-3.02540.37141580.32343077346698
3.0254-3.81120.25771560.229931923348100
3.8112-41.10340.23071680.21023298323599

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