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- PDB-3l9a: Structure of the C-terminal domain from a Streptococcus mutans hy... -

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Basic information

Entry
Database: PDB / ID: 3l9a
TitleStructure of the C-terminal domain from a Streptococcus mutans hypothetical
Componentsuncharacterized protein
Keywordsstructural genomics / unknown function / phage-associated / hypothetical protein / CHAP domain / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologySignal recognition particle alu RNA binding heterodimer, srp9/1 - #180 / CHAP domain profile. / CHAP domain / CHAP domain / Signal recognition particle alu RNA binding heterodimer, srp9/1 / Papain-like cysteine peptidase superfamily / 2-Layer Sandwich / Alpha Beta / Peptidase C51 domain-containing protein
Function and homology information
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsSinger, A.U. / Cuff, M.E. / Xu, X. / Cui, H. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of the C-terminal domain from a Streptococcus mutans hypothetical
Authors: Singer, A.U. / Cuff, M.E. / Xu, X. / Cui, H. / Edwards, A.M. / Savchenko, A.
History
DepositionJan 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5003
Polymers10,3851
Non-polymers1152
Water2,288127
1
X: uncharacterized protein
hetero molecules

X: uncharacterized protein
hetero molecules

X: uncharacterized protein
hetero molecules

X: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,99912
Polymers41,5384
Non-polymers4608
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area7650 Å2
ΔGint-43 kcal/mol
Surface area13760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.080, 64.080, 39.975
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Detailstetramer is made of molecule 1 -- the solved molecule rotation matrix transl vector molecule 2 -- (0.000 1.000 0.000 (0.000 -1.000 0.000 0.000 64.08 0.000 0.000 1.000) 0.000) molecule 3 -- (0.000 -1.000 0.000 (64.08 1.000 0.000 0.000 0.000 0.000 0.000 1.000) 0.000) molecule 4 -- (-1.00 0.000 0.000 (64.08 0.000 -1.00 0.000 64.08 0.000 0.000 1.000) 0.000)

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Components

#1: Protein uncharacterized protein


Mass: 10384.569 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: papain cleavage / Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: OM98x / Gene: BAF47173 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: A2V8B8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 127 / 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: 1.98 Å3/Da / Density % sol: 37.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes ph7.5, 0.2M Ammonium Sulfate, 25% PEG3350, 1/10 Papain. Cryoprotected with crystallization solution plus 8% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97915, 0.97942
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2009 / Details: mirrors
RadiationMonochromator: SI-111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979151
20.979421
ReflectionResolution: 1.25→23.29 Å / Num. all: 22544 / Num. obs: 20493 / % possible obs: 90.9 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 9 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 59.333
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 10.5 / Num. unique all: 567 / % possible all: 49.9

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Processing

Software
NameVersionClassification
HKL-3000data collection
SHELXCDphasing
SHELXEmodel building
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD
Starting model: none

Resolution: 1.3→23.29 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.029 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1549 990 5.2 %RANDOM
Rwork0.13354 ---
obs0.13462 19106 95.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.877 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.3→23.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms743 0 19 136 898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022783
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.161.9191064
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.382596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.83924.63441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.21315133
X-RAY DIFFRACTIONr_dihedral_angle_4_deg34.183153
X-RAY DIFFRACTIONr_chiral_restr0.0870.2111
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02611
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.240.2364
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.2556
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.299
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.080.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.264
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7981.5453
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2992747
X-RAY DIFFRACTIONr_scbond_it1.9683339
X-RAY DIFFRACTIONr_scangle_it2.6354.5316
X-RAY DIFFRACTIONr_rigid_bond_restr1.5863792
X-RAY DIFFRACTIONr_sphericity_free3.7533137
X-RAY DIFFRACTIONr_sphericity_bonded2.0083761
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.195 64 -
Rwork0.15 984 -
obs-1048 71.34 %

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