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- PDB-3gng: P21B crystal structure of R1-R7 of Murine MVP -

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Basic information

Entry
Database: PDB / ID: 3gng
TitleP21B crystal structure of 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 / Resolution: 3 Å
AuthorsQuerol-Audi, J. / Casanas, A. / Uson, I. / 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: Advisory / 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
A: Major vault protein


Theoretical massNumber of molelcules
Total (without water)43,7361
Polymers43,7361
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.776, 60.087, 68.628
Angle α, β, γ (deg.)90.00, 95.34, 90.00
Int Tables number4
Space group name H-MP1211

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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

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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: 2.76 Å3/Da / Density % sol: 55.42 %
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 315 / 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: 3→30 Å / Num. all: 8990 / Num. obs: 8896 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 3→3.077 Å / % possible all: 95.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GF5

3gf5


Resolution: 3→29.7 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.849 / SU B: 52.192 / SU ML: 0.435 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.51 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28703 454 4.9 %RANDOM
Rwork0.25705 ---
obs0.25844 8896 96.57 %-
all-8990 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.395 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å20.48 Å2
2--0.31 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 3→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2959 0 0 0 2959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0223014
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7681.9724101
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3415370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40724.178146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4915516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.1191525
X-RAY DIFFRACTIONr_chiral_restr0.0430.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.022303
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1380.21055
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.290.21997
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0730.257
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0990.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0231.51944
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.04123022
X-RAY DIFFRACTIONr_scbond_it0.05931226
X-RAY DIFFRACTIONr_scangle_it0.1044.51079
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 37 -
Rwork0.369 621 -
obs--95.5 %
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)
113.2097-0.0311-6.98031.75881.83936.28010.0325-0.70880.0354-0.1322-0.14170.2609-0.2691-0.28380.1092-0.1078-0.0406-0.1281-0.1393-0.0155-0.124-40.5071.280138.8364
211.4547-4.1583-5.34973.962.58173.81610.0896-0.97570.8510.21120.1559-0.2437-0.28220.4188-0.24550.0568-0.0786-0.088-0.0364-0.07880.0609-21.96334.668435.4281
35.0846-1.3751-1.63475.67822.98449.24290.1412-0.25850.22710.0932-0.034-0.4859-0.07740.169-0.1072-0.1689-0.0272-0.0241-0.1445-0.06290.0029-0.87074.230829.2276
46.4803-1.4407-4.24556.87972.12375.15120.0330.38750.0129-0.2384-0.16820.23620.08140.0510.13520.0136-0.0390.0569-0.02330.0147-0.006517.8529-0.549216.9127
56.4898-1.4406-3.48027.84392.71144.9943-0.03640.0626-0.13340.1143-0.2415-0.339-0.0425-0.04520.27790.11580.05880.06580.20080.12650.047735.2752-1.11856.2661
69.6357-4.6422-7.14577.80562.38875.8335-0.3028-0.64470.27320.46230.5932-0.0318-0.19420.4588-0.29040.18180.00550.06160.20480.06620.078252.0077-2.5193-6.1629
77.70791.428-1.777512.87030.57798.4750.1088-0.5390.16990.73650.2033-0.2645-0.20810.4314-0.31210.0128-0.06230.03820.1787-0.088-0.011469.1744-3.7397-16.4304
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 53
2X-RAY DIFFRACTION2A56 - 115
3X-RAY DIFFRACTION3A118 - 163
4X-RAY DIFFRACTION4A164 - 221
5X-RAY DIFFRACTION5A222 - 276
6X-RAY DIFFRACTION6A279 - 326
7X-RAY DIFFRACTION7A328 - 380

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