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- PDB-3fb9: The crystal structure of the protein with unknown function from S... -

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Basic information

Entry
Database: PDB / ID: 3fb9
TitleThe crystal structure of the protein with unknown function from Streptococcus pneumoniae TIGR4
Componentsuncharacterized protein
Keywordsstructural genomics / unknown function / MCSG / PSI2 / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homologyProtein Veg / Biofilm formation stimulator VEG / SH3 type barrels. - #100 / SH3 type barrels. / Roll / regulation of DNA-templated transcription / Mainly Beta / PF06257 family protein / Uncharacterized protein
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsZhang, R. / Li, H. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the protein with unknown function from Streptococcus pneumoniae TIGR4
Authors: Zhang, R. / Li, H. / Abdullah, J. / Joachimiak, A.
History
DepositionNov 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Dec 27, 2023Group: 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

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Assembly

Deposited unit
A: uncharacterized protein
B: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)20,8242
Polymers20,8242
Non-polymers00
Water3,567198
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.609, 53.118, 72.036
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


Mass: 10411.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: GI:14973714, SP_2202 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q97N65, UniProt: A0A0H2US72*PLUS
#2: 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: 2.14 Å3/Da / Density % sol: 42.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M NaCl, 0.1M Tris, 25%PEG3350, pH 7.5, 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 315 / Detector: CCD / Date: Oct 3, 2007 / Details: mirrors
RadiationMonochromator: Si channel 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.8→42.76 Å / Num. all: 16314 / Num. obs: 16247 / % possible obs: 99.59 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.4 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 29.64
Reflection shellResolution: 1.8→1.846 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 8.14 / Num. unique all: 1248 / % possible all: 97.2

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→42.76 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.635 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.141 / ESU R Free: 0.135
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23436 868 5.1 %RANDOM
Rwork0.19073 ---
obs0.19297 16247 99.59 %-
all-16314 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.274 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å20 Å20 Å2
2--1.77 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1399 0 0 198 1597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221418
X-RAY DIFFRACTIONr_bond_other_d0.0010.02967
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.9711900
X-RAY DIFFRACTIONr_angle_other_deg0.90532381
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8835170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41125.94269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32315283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.39154
X-RAY DIFFRACTIONr_chiral_restr0.0970.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021536
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02264
X-RAY DIFFRACTIONr_mcbond_it1.2171.5853
X-RAY DIFFRACTIONr_mcbond_other0.3661.5353
X-RAY DIFFRACTIONr_mcangle_it2.28621380
X-RAY DIFFRACTIONr_scbond_it3.5813565
X-RAY DIFFRACTIONr_scangle_it5.764.5520
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 54 -
Rwork0.208 1159 -
obs-1213 97.2 %
Refinement TLS params.Method: refined / Origin x: 23.539 Å / Origin y: 2.27 Å / Origin z: 24.486 Å
111213212223313233
T0.0705 Å20.0019 Å2-0.0066 Å2-0.0849 Å2-0.0052 Å2--0.0697 Å2
L0.3564 °20.0366 °2-0.5946 °2-0.0688 °2-0.1304 °2--1.2998 °2
S-0.0793 Å °-0.0472 Å °-0.0256 Å °0.0047 Å °0.0156 Å °-0.0125 Å °0.0231 Å °0.0615 Å °0.0637 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 88
2X-RAY DIFFRACTION1B-1 - 31
3X-RAY DIFFRACTION1B38 - 88

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