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- PDB-2jbx: Crystal Structure of the myxoma virus anti-apoptotic protein M11L -

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Basic information

Entry
Database: PDB / ID: 2jbx
TitleCrystal Structure of the myxoma virus anti-apoptotic protein M11L
ComponentsM11L PROTEIN
KeywordsAPOPTOSIS / BCL-2 FAMILY / MYXOMA VIRUS
Function / homology
Function and homology information


symbiont-mediated suppression of host apoptosis / regulation of apoptotic process / membrane
Similarity search - Function
Poxvirus F1/C10 / Apoptosis regulator M11L like / Blc2-like / Apoptosis Regulator Bcl-x / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Apoptosis regulator M11L
Similarity search - Component
Biological speciesMYXOMA VIRUS
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsKvansakul, M. / Van Delft, M.F. / Lee, E.F. / Gulbis, J.M. / Fairlie, W.D. / Huang, D.C.S. / Colman, P.M.
CitationJournal: Mol.Cell / Year: 2007
Title: A Structural Viral Mimic of Prosurvival Bcl-2: A Pivotal Role for Sequestering Proapoptotic Bax and Bak.
Authors: Kvansakul, M. / Van Delft, M.F. / Lee, E.F. / Gulbis, J.M. / Fairlie, W.D. / Huang, D.C.S. / Colman, P.M.
History
DepositionDec 14, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: M11L PROTEIN
B: M11L PROTEIN


Theoretical massNumber of molelcules
Total (without water)33,7632
Polymers33,7632
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-11.2 kcal/mol
Surface area15740 Å2
MethodPQS
Unit cell
Length a, b, c (Å)39.876, 39.398, 49.222
Angle α, β, γ (deg.)71.79, 90.09, 81.66
Int Tables number1
Space group name H-MP1

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Components

#1: Protein M11L PROTEIN / M11L / APOPTOSIS REGULATOR M11L


Mass: 16881.328 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYXOMA VIRUS / Strain: LAUSANNE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYZ / References: UniProt: Q85295
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.19 Å3/Da / Density % sol: 43.82 % / Description: PDB ENTRY FOR M11L BAK COMPLEX TO BE SUBMITTED
Crystal growpH: 7.2
Details: 1.8 M AMMONIUM SULFATE, 10 MM KSCN, 100 MM HEPES PH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Dec 7, 2005 / Details: AXCO CAPILLARY OPTICS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.73→20 Å / Num. obs: 7483 / % possible obs: 97.3 % / Observed criterion σ(I): 3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9
Reflection shellResolution: 2.73→2.83 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3 / % possible all: 91.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: M11L BAK COMPLEX

Resolution: 2.73→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.839 / SU B: 18.914 / SU ML: 0.387 / Cross valid method: THROUGHOUT / ESU R Free: 0.445 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.286 373 5.1 %RANDOM
Rwork0.214 ---
obs0.218 6895 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.84 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å20.39 Å20.38 Å2
2---0.7 Å2-1.3 Å2
3---2.46 Å2
Refinement stepCycle: LAST / Resolution: 2.73→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 0 67 2126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222075
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.871.9732810
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3645259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2226.37491
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.34415392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.873156
X-RAY DIFFRACTIONr_chiral_restr0.1450.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021493
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3110.21253
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3280.21474
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2118
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2830.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.49121331
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.30232113
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7985833
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.5387696
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.73→2.8 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.415 23
Rwork0.276 457

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