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- PDB-2bvu: D83R mutant of Asaris suum major sperm protein (MSP) -

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Basic information

Entry
Database: PDB / ID: 2bvu
TitleD83R mutant of Asaris suum major sperm protein (MSP)
ComponentsMAJOR SPERM PROTEIN, ISOFORM ALPHA
KeywordsSTRUCTURAL PROTEIN / CYTOSKETAL PROTEIN / MAJOR SPERM PROTEIN
Function / homology
Function and homology information


pseudopodium / cytoskeleton / cytoplasm
Similarity search - Function
: / Major sperm protein (MSP) domain / MSP (Major sperm protein) domain / Major sperm protein (MSP) domain profile. / PapD-like superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Major sperm protein isoform alpha
Similarity search - Component
Biological speciesASCARIS SUUM (pig roundworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsStewart, M. / Grant, R.P. / Roberts, T.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: The Role of Filament-Packing Dynamics in Powering Amoeboid Cell Motility.
Authors: Miao, L. / Vanderlinde, O. / Liu, J. / Grant, R.P. / Wouterse, A. / Shimabukuro, K. / Philipse, A. / Stewart, M. / Roberts, T.M.
History
DepositionJul 4, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Refinement description / Category: software
Revision 1.4Dec 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MAJOR SPERM PROTEIN, ISOFORM ALPHA
B: MAJOR SPERM PROTEIN, ISOFORM ALPHA
C: MAJOR SPERM PROTEIN, ISOFORM ALPHA
D: MAJOR SPERM PROTEIN, ISOFORM ALPHA


Theoretical massNumber of molelcules
Total (without water)57,2814
Polymers57,2814
Non-polymers00
Water2,738152
1
A: MAJOR SPERM PROTEIN, ISOFORM ALPHA


Theoretical massNumber of molelcules
Total (without water)14,3201
Polymers14,3201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: MAJOR SPERM PROTEIN, ISOFORM ALPHA


Theoretical massNumber of molelcules
Total (without water)14,3201
Polymers14,3201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: MAJOR SPERM PROTEIN, ISOFORM ALPHA


Theoretical massNumber of molelcules
Total (without water)14,3201
Polymers14,3201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: MAJOR SPERM PROTEIN, ISOFORM ALPHA


Theoretical massNumber of molelcules
Total (without water)14,3201
Polymers14,3201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)54.805, 54.805, 453.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
MAJOR SPERM PROTEIN, ISOFORM ALPHA / ALPHA-MSP


Mass: 14320.215 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASCARIS SUUM (pig roundworm) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): PET / References: UniProt: P27439
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 83 TO ARG ENGINEERED RESIDUE IN CHAIN B, ASP 83 TO ARG ...ENGINEERED RESIDUE IN CHAIN A, ASP 83 TO ARG ENGINEERED RESIDUE IN CHAIN B, ASP 83 TO ARG ENGINEERED RESIDUE IN CHAIN C, ASP 83 TO ARG ENGINEERED RESIDUE IN CHAIN D, ASP 83 TO ARG

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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: 2.97 Å3/Da / Density % sol: 58.59 %
Crystal growDetails: PROTEIN 5 MG/ML; 15% PEG4000; 0.1M AMMONIUM ACETATE (PH 5.9); 2% AMMONIUM SULPHATE; 10 MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC / Date: Sep 18, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 17093 / % possible obs: 93.3 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.9
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4.7 / % possible all: 78.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GRW

1grw


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.889 / SU B: 11.914 / SU ML: 0.252 / Cross valid method: THROUGHOUT / ESU R: 0.466 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.291 1221 5.2 %RANDOM
Rwork0.226 ---
obs0.23 22317 92.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 56.07 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å20 Å20 Å2
2--1.16 Å20 Å2
3----2.31 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3829 0 0 152 3981
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223921
X-RAY DIFFRACTIONr_bond_other_d0.0010.023500
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.9425341
X-RAY DIFFRACTIONr_angle_other_deg0.70238132
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2645489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.19724.157178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.64815627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3141529
X-RAY DIFFRACTIONr_chiral_restr0.0880.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024383
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02769
X-RAY DIFFRACTIONr_nbd_refined0.2340.3864
X-RAY DIFFRACTIONr_nbd_other0.2270.33755
X-RAY DIFFRACTIONr_nbtor_refined0.1930.51834
X-RAY DIFFRACTIONr_nbtor_other0.0980.52505
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2410.5235
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1020.55
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3270.325
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2920.390
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3690.515
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.53152543
X-RAY DIFFRACTIONr_mcbond_other0.5695990
X-RAY DIFFRACTIONr_mcangle_it5.408103997
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.464101609
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.039201344
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: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 19 -
Rwork0.395 1286 -
obs--74.44 %

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