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- PDB-1pg6: X-Ray Crystal Structure of Protein SPYM3_0169 from Streptococcus ... -

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Basic information

Entry
Database: PDB / ID: 1pg6
TitleX-Ray Crystal Structure of Protein SPYM3_0169 from Streptococcus pyogenes. Northeast Structural Genomics Consortium Target DR2.
ComponentsHypothetical protein SpyM3_0169
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Streptococcus pyogenes / SpyM3_0169 / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyDouble-stranded beta-helix / Mitochondrial biogenesis AIM24 / 4-Layer Sandwich / Alpha Beta / :
Function and homology information
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsKuzin, A. / Lee, I. / Edstrom, W. / Xiao, R. / Acton, T. / Rost, B. / Montelione, G. / Hunt, J. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published / Year: 2003
Title: X-ray structure of hypothetical protein SPYM3_0169 from Streptococcus pyogenes
Authors: Kuzin, A. / Lee, I. / Edstrom, W. / Xiao, R. / Acton, T. / Rost, B. / Montelione, G. / Hunt, J. / Tong, L.
History
DepositionMay 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein SpyM3_0169
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0583
Polymers26,9781
Non-polymers802
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Hypothetical protein SpyM3_0169
hetero molecules

A: Hypothetical protein SpyM3_0169
hetero molecules

A: Hypothetical protein SpyM3_0169
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1749
Polymers80,9333
Non-polymers2406
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area8790 Å2
ΔGint-141 kcal/mol
Surface area29030 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.541, 71.541, 216.927
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Cell settingtrigonal
Space group name H-MH32

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Components

#1: Protein Hypothetical protein SpyM3_0169 / Hypothetical protein spyM18_0222


Mass: 26977.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: all methionines modified to SeMet / Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: MGAS8232 / Gene: SPS0176 / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8P2Q3
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.06 Å3/Da / Density % sol: 39.8 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: CaCl2, HEPES-Na, PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9800, 0.9802, 0.9720
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 11, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
20.98021
30.9721
ReflectionResolution: 1.7→20 Å / Num. all: 45195 / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.2 Å2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→19.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 333852.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2063 5 %RANDOM
Rwork0.213 ---
obs0.2131 40990 90 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.0468 Å2 / ksol: 0.36361 e/Å3
Displacement parametersBiso mean: 27.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å2-0.41 Å20 Å2
2---1.69 Å20 Å2
3---3.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1650 0 2 182 1834
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d0.58
X-RAY DIFFRACTIONc_mcbond_it1.451.5
X-RAY DIFFRACTIONc_mcangle_it2.42
X-RAY DIFFRACTIONc_scbond_it2.522
X-RAY DIFFRACTIONc_scangle_it3.592.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.237 286 5.1 %
Rwork0.225 5280 -
obs--73.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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