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- PDB-3gnf: P1 Crystal structure of the N-terminal R1-R7 of murine MVP -

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Basic information

Entry
Database: PDB / ID: 3gnf
TitleP1 Crystal structure of the N-terminal R1-R7 of murine MVP
ComponentsMajor vault protein
KeywordsSTRUCTURAL PROTEIN / beta sheets / Phosphoprotein / Ribonucleoprotein
Function / homology
Function and homology information


protein activation cascade / negative regulation of protein autophosphorylation / ERBB signaling pathway / negative regulation of epidermal growth factor receptor signaling pathway / Neutrophil degranulation / protein phosphatase binding / cell population proliferation / cytoskeleton / ribonucleoprotein complex / protein kinase binding ...protein activation cascade / negative regulation of protein autophosphorylation / ERBB signaling pathway / negative regulation of epidermal growth factor receptor signaling pathway / Neutrophil degranulation / protein phosphatase binding / cell population proliferation / cytoskeleton / ribonucleoprotein complex / protein kinase binding / perinuclear region of cytoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Major vault protein, N-terminal structural repeat domain / SH3 type barrels. - #570 / Major Vault Protein repeat / Major vault protein, N-terminal / Major vault protein, shoulder domain / Major vault protein / Major vault protein repeat domain 3 / Major vault protein repeat domain 2 / Major vault protein repeat domain 4 / Major vault protein repeat domain ...Major vault protein, N-terminal structural repeat domain / SH3 type barrels. - #570 / Major Vault Protein repeat / Major vault protein, N-terminal / Major vault protein, shoulder domain / Major vault protein / Major vault protein repeat domain 3 / Major vault protein repeat domain 2 / Major vault protein repeat domain 4 / Major vault protein repeat domain / Major vault protein repeat domain superfamily / Major vault protein repeat domain 2 superfamily / Major Vault Protein repeat domain / Shoulder domain / Major Vault Protein repeat domain / Major Vault Protein Repeat domain / Major Vault Protein repeat domain / MVP (vault) repeat profile. / Band 7/SPFH domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / MAD / Resolution: 2.1 Å
AuthorsQuerol-Audi, J. / Casanas, A. / Uson, I. / Luque, D. / Caston, J.R. / Fita, I. / Verdaguer, N.
CitationJournal: Embo J. / Year: 2009
Title: The mechanism of vault opening from the high resolution structure of the N-terminal repeats of MVP
Authors: Querol-Audi, J. / Casanas, A. / Uson, I. / Luque, D. / Caston, J.R. / Fita, I. / Verdaguer, N.
History
DepositionMar 17, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Major vault protein


Theoretical massNumber of molelcules
Total (without water)43,7361
Polymers43,7361
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.562, 51.892, 79.338
Angle α, β, γ (deg.)101.69, 92.28, 99.41
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Major vault protein / / MVP


Mass: 43735.777 Da / Num. of mol.: 1 / Fragment: R1-R7 domain, UNP residues 1-383
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mvp / Plasmid: pGex-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9EQK5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20%PEG 5000, 0.1M Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 12, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 26128 / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.031 / Net I/σ(I): 14.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
DMphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GF5

3gf5


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.912 / Occupancy max: 1 / Occupancy min: 1 / SU B: 14.049 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.255 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27622 1256 5 %RANDOM
Rwork0.23754 ---
obs0.23952 23954 95.16 %-
all-16870 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.566 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20.93 Å21.63 Å2
2--0.76 Å24 Å2
3---2.29 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2896 0 0 59 2955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222957
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2641.9734022
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6795363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.21423.873142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.44315505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0421526
X-RAY DIFFRACTIONr_chiral_restr0.0870.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022260
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.21075
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21924
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2122
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5151.51874
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.89422962
X-RAY DIFFRACTIONr_scbond_it1.45231206
X-RAY DIFFRACTIONr_scangle_it2.3974.51060
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 64 -
Rwork0.291 1335 -
obs--71.97 %

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