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- PDB-1pm4: Crystal structure of Yersinia pseudotuberculosis-derived mitogen (YPM) -

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Basic information

Entry
Database: PDB / ID: 1pm4
TitleCrystal structure of Yersinia pseudotuberculosis-derived mitogen (YPM)
ComponentsYPM
KeywordsTOXIN / Jelly roll fold
Function / homologyMitogen Ypm / Mitogen, Yersinia pseudotuberculosis / Mitogen Ypm superfamily / Yersinia pseudo-tuberculosis mitogen / Jelly Rolls / Sandwich / Mainly Beta / -derived mitogen
Function and homology information
Biological speciesYersinia pseudotuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.755 Å
AuthorsDonadini, R. / Liew, C.W. / Kwan, A.H. / Mackay, J.P. / Fields, B.A.
CitationJournal: Structure / Year: 2004
Title: Crystal and Solution Structures of a Superantigen from Yersinia pseudotuberculosis Reveal a Jelly-Roll Fold.
Authors: Donadini, R. / Liew, C.W. / Kwan, A.H. / Mackay, J.P. / Fields, B.A.
History
DepositionJun 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). The trimerization may be biologically relevant but has not yet been established experimentally. The protein is a monomer in solution.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YPM
B: YPM
C: YPM


Theoretical massNumber of molelcules
Total (without water)39,6713
Polymers39,6713
Non-polymers00
Water6,107339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.651, 78.652, 32.901
Angle α, β, γ (deg.)90.00, 91.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein YPM


Mass: 13223.785 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Gene: ypma / Plasmid: pMAL-p2x / Production host: Escherichia coli (E. coli) / Strain (production host): Novablue / References: UniProt: Q57221
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.26 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: Ammonium sulfate, PEG 200, sodium citrate, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 293 K / pH: 7.2 / Method: vapor diffusion, sitting drop / Details: Donadini, R., (2003) Acta Cryst., D59, 1330.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.95-2.10 Mammonium sulfate1reservoir
24-5 %(v/v)PEG2001reservoir
30.1 Msodium citrate1reservoirpH5.8-7.6
475 mg/mlprotein1drop
50.1 Msodium citrate1droppH7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.071 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 12, 2002
RadiationMonochromator: 2-crystal monochromator, Si111, 1m long Rh coated bent cylindrical mirror for horizontal and vertical focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.071 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. all: 253851 / Num. obs: 253092 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 39.1
Reflection shellResolution: 1.755→1.8 Å / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 3.2 / % possible all: 99.1
Reflection
*PLUS
Num. obs: 35166 / Num. measured all: 253092
Reflection shell
*PLUS
Highest resolution: 1.75 Å / % possible obs: 99.1 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.755→34.71 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.441 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.125 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22926 1749 5 %RANDOM
Rwork0.18201 ---
all0.18438 35113 --
obs0.18438 33364 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.498 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å2-0.9 Å2
2--0.07 Å20 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 1.755→34.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2748 0 0 339 3087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0212799
X-RAY DIFFRACTIONr_bond_other_d0.0020.022450
X-RAY DIFFRACTIONr_angle_refined_deg1.8971.9513796
X-RAY DIFFRACTIONr_angle_other_deg0.93235759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8365348
X-RAY DIFFRACTIONr_chiral_restr0.120.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023104
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02504
X-RAY DIFFRACTIONr_nbd_refined0.2270.2544
X-RAY DIFFRACTIONr_nbd_other0.2630.22966
X-RAY DIFFRACTIONr_nbtor_other0.0880.21765
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2242
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1260.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3080.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.222
X-RAY DIFFRACTIONr_mcbond_it1.3981.51732
X-RAY DIFFRACTIONr_mcangle_it2.39322803
X-RAY DIFFRACTIONr_scbond_it2.83331067
X-RAY DIFFRACTIONr_scangle_it4.24.5993
LS refinement shellResolution: 1.755→1.8 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.256 124
Rwork0.222 2350
Refinement
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 40 Å / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.021
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.9
LS refinement shell
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 1.8 Å

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