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- PDB-2qsv: Crystal structure of protein of unknown function from Porphyromon... -

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Basic information

Entry
Database: PDB / ID: 2qsv
TitleCrystal structure of protein of unknown function from Porphyromonas gingivalis W83
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / MCSG / Porphyromonas gingivalis W83 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


cysteine-type peptidase activity / proteolysis
Similarity search - Function
Protein of unknown function DUF1573 / : / Protein of unknown function (DUF1573) / PG_0320-like, C-terminal domain / : / HYDIN/CFA65/VesB-like, Ig-like domain / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DUF1573 domain-containing protein
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsBinkowski, T.A. / Duggan, E. / Shui, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Protein of unknown function from Porphyromonas gingivalis W83.
Authors: Binkowski, T.A. / Duggan, E. / Shui, M. / Joachimiak, A.
History
DepositionJul 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Remark 300 BIOMOLECULE: 1 SEE REMARK 350 FOR THE PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS POLYPEPTIDE IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1943
Polymers24,0751
Non-polymers1192
Water3,567198
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.237, 107.237, 59.833
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-189-

LYS

DetailsAuthors state that the biological unit of this protein is unknown

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Components

#1: Protein Uncharacterized protein


Mass: 24074.547 Da / Num. of mol.: 1 / Fragment: C-terminal part: Residues 143-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: PG_0320 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7MX90
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 4.18 Å3/Da / Density % sol: 70.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Saturated sucrose, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97945 Å
DetectorType: SBC-2 / Detector: CCD / Date: Jun 2, 2007
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.1→92.85 Å / Num. all: 23401 / Num. obs: 22139 / % possible obs: 94.6 % / Observed criterion σ(I): 2
Reflection shellResolution: 2.1→2.18 Å / % possible all: 48.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→46.42 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.79 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23285 1196 5.1 %RANDOM
Rwork0.20382 ---
obs0.20526 22139 99.71 %-
all-22139 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.671 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20.48 Å20 Å2
2--0.95 Å20 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1661 0 6 198 1865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221771
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6582.0052422
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6455235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.58124.30672
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.46915316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5691517
X-RAY DIFFRACTIONr_chiral_restr0.1080.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021337
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2380.2745
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21157
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2187
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.3220.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0871.51148
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.98121882
X-RAY DIFFRACTIONr_scbond_it2.8273629
X-RAY DIFFRACTIONr_scangle_it4.7494.5538
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 83 -
Rwork0.241 1595 -
obs--98.71 %

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