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- PDB-4d8e: High resolution structures of monomeric S. pyogenes SpeB reveals ... -

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Basic information

Entry
Database: PDB / ID: 4d8e
TitleHigh resolution structures of monomeric S. pyogenes SpeB reveals role of glycine-rich active site loop
ComponentsStreptopain
KeywordsHYDROLASE / papain fold / cysteine protease / E64 complex / secreted
Function / homologyStreptopain (SpeB) / Cathepsin B; Chain A / Alpha-Beta Complex / Alpha Beta / Chem-E64 / NITRATE ION / :
Function and homology information
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.497 Å
AuthorsGonzalez, G.E. / Wolan, D.W.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Ultrahigh and High Resolution Structures and Mutational Analysis of Monomeric Streptococcus pyogenes SpeB Reveal a Functional Role for the Glycine-rich C-terminal Loop.
Authors: Gonzalez-Paez, G.E. / Wolan, D.W.
History
DepositionJan 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Aug 1, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Streptopain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1664
Polymers28,6821
Non-polymers4843
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.606, 50.675, 37.384
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-656-

HOH

21A-702-

HOH

31A-820-

HOH

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Components

#1: Protein Streptopain


Mass: 28681.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: ATCC 10782 / Gene: HMPREF0841_0152, speB / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: E0PTS8, streptopain
#2: Chemical ChemComp-E64 / N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE


Mass: 360.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H30N5O5
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 1.89 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Magnesium Nitrate, 20% PEG3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2011 / Details: Mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.497→35.541 Å / Num. all: 35934 / Num. obs: 35933 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 23.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.497-1.5350.5731.7195.5
1.53-1.554.70.532.1197.6
1.55-1.584.50.4832.6199.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SOLVEphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.497→35.541 Å / SU ML: 0.21 / σ(F): 0.33 / Phase error: 18.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1877 1773 4.99 %
Rwork0.1581 --
obs0.1596 35508 98.81 %
all-35699 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.005 Å2 / ksol: 0.385 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1295 Å20 Å20 Å2
2---0.2464 Å2-0 Å2
3---0.117 Å2
Refinement stepCycle: LAST / Resolution: 1.497→35.541 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 0 33 383 2374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.022051
X-RAY DIFFRACTIONf_angle_d1.8542780
X-RAY DIFFRACTIONf_dihedral_angle_d12.837733
X-RAY DIFFRACTIONf_chiral_restr0.133283
X-RAY DIFFRACTIONf_plane_restr0.011373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.497-1.53770.34031060.30492370X-RAY DIFFRACTION91
1.5377-1.5830.27811420.24442519X-RAY DIFFRACTION99
1.583-1.63410.27051350.21812569X-RAY DIFFRACTION99
1.6341-1.69250.2521280.19552582X-RAY DIFFRACTION99
1.6925-1.76020.22111300.17772577X-RAY DIFFRACTION100
1.7602-1.84040.20791360.15832585X-RAY DIFFRACTION100
1.8404-1.93740.19511300.15272582X-RAY DIFFRACTION100
1.9374-2.05870.19881510.14612595X-RAY DIFFRACTION100
2.0587-2.21770.1811350.14252621X-RAY DIFFRACTION99
2.2177-2.44080.16111460.13632606X-RAY DIFFRACTION100
2.4408-2.79390.16421350.14832647X-RAY DIFFRACTION100
2.7939-3.51950.17671340.14232687X-RAY DIFFRACTION100
3.5195-35.55090.16451650.1512795X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.61780.03810.05210.52390.01390.8244-0.01280.0597-0.0483-0.00590.02310.0216-0.0176-0.0084-0.01430.07460.00260.00190.0964-0.01480.0755-20.637414.05042.9553
21.19160.8408-0.15661.2562-0.91591.38880.1293-0.2962-0.01310.237-0.06250.0546-0.13830.213-0.08370.12860.01620.00710.0986-0.02130.093-6.841517.449212.9879
30.66410.10370.31560.741-0.56730.7841-0.05510.08650.1142-0.06730.01-0.0255-0.04440.0390.05090.11830.0043-0.00240.1278-0.00170.1366-8.418726.7554-0.9843
41.6465-0.09910.38271.2322-0.00411.12580.0123-0.27720.04530.0033-0.00160.05470.0396-0.16-0.00610.110.0098-0.00460.0969-0.00540.0858-23.61416.486816.1251
51.7801-0.0943-1.14770.16660.21781.06180.01320.02910.03910.0366-0.00570.0224-0.1057-0.0602-0.03420.1244-0.0019-0.00490.10230.00240.0974-17.980219.717510.3624
60.6031-0.16070.14180.93450.22070.4930.00220.0124-0.0347-0.02320.0333-0.09030.0453-0.0004-0.03390.0859-0.0012-0.0040.10560.00080.1105-6.13068.03163.5094
71.1325-0.2575-0.35561.4580.05340.7797-0.02910.0432-0.2075-0.02770.08260.04430.1737-0.0405-0.05310.0838-0.0094-0.01920.0782-0.00630.1275-11.8618-4.34772.5707
80.96250.2742-0.02750.66280.35471.3099-0.02240.1584-0.0786-0.1688-0.00980.02730.0341-0.11760.0020.048-0.003-0.00020.0378-0.01190.0578-22.1057-1.2636-2.7407
91.5850.04651.00570.90240.31042.94590.0260.1196-0.004-0.05490.0527-0.0634-0.00780.1225-0.0380.0659-0.0022-0.00220.0390.00070.0698-10.65451.18180.659
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 146:204)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 205:217)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 218:237)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 238:254)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 255:272)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 273:311)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 312:337)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 338:382)
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 383:399)

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