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- PDB-3kph: Crystal structure of Mycoplasma arthritidis-derived mitogen -

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Basic information

Entry
Database: PDB / ID: 3kph
TitleCrystal structure of Mycoplasma arthritidis-derived mitogen
ComponentsSuperantigen
KeywordsIMMUNE SYSTEM / superantigen / MAM / 3D-domain swap
Function / homology
Function and homology information


mam-mhc complex, Chain D, Domain 2 / Hla class ii histocompatibility antigen, dr alpha chain. Chain D, domain 1 / Mycoplasma arthritidis-derived mitogen / Superantigen MAM / Mycoplasma arthritidis-derived mitogen, C-terminal / Mycoplasma arthritidis-derived mitogen / Four Helix Bundle (Hemerythrin (Met), subunit A) / Arc Repressor Mutant, subunit A / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Superantigen
Similarity search - Component
Biological speciesMycoplasma arthritidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLiu, L.H. / Li, H.M.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal Structure of the Mycoplasma arthritidis-Derived Mitogen in Apo Form Reveals a 3D Domain-Swapped Dimer.
Authors: Liu, L. / Li, Z. / Guo, Y. / Vanvranken, S.J. / Mourad, W. / Li, H.
History
DepositionNov 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Superantigen
B: Superantigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4265
Polymers51,1412
Non-polymers2853
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-42.8 kcal/mol
Surface area20720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.865, 181.865, 181.865
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11B-601-

HOH

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Components

#1: Protein Superantigen /


Mass: 25570.594 Da / Num. of mol.: 2 / Fragment: UNP residues 26-239 / Mutation: K201A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma arthritidis (bacteria) / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q48898
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 4.9 Å3/Da / Density % sol: 74.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.2
Details: 13-15% PEG 3350, 0.2 M NaCl, 5% Ethylene glycol, 5% Glycerol, 0.1 M Potassium/sodium phosphate pH 6.2, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.2757 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 10, 2004 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2757 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 24867 / Num. obs: 24867 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 6.93 % / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 9.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.692 / % possible all: 96.8

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Processing

Software
NameVersionClassificationNB
CNS1refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1R5I

1r5i


Resolution: 2.8→50 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 2330671 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.299 1263 5.1 %RANDOM
Rwork0.253 ---
all0.253 24853 --
obs0.253 24853 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.483 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso max: 133.23 Å2 / Biso mean: 69.238 Å2 / Biso min: 19.64 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.66 Å
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3259 0 15 62 3336
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d19.2
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.42
X-RAY DIFFRACTIONc_scbond_it1.792
X-RAY DIFFRACTIONc_scangle_it2.942.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.411 213 5.2 %
Rwork0.378 3859 -
all-4072 -
obs--96.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ion.paramion.top

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