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- PDB-2msp: MAJOR SPERM PROTEIN, BETA ISOFORM, ENGINEERED C59S/T90C MUTANT, P... -

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Basic information

Entry
Database: PDB / ID: 2msp
TitleMAJOR SPERM PROTEIN, BETA ISOFORM, ENGINEERED C59S/T90C MUTANT, PUTATIVE SUBFILAMENT STRUCTURE, PH 8.5
ComponentsMAJOR SPERM PROTEIN
KeywordsCELL MOTILITY PROTEIN / CYTOSKELETAL PROTEIN / NEMATODE SPERM CELL MOTILITY PROTEIN / FILAMENTOUS PROTEIN STRUCTURE
Function / homology
Function and homology information


pseudopodium / cytoskeleton / identical protein binding / cytoplasm
Similarity search - Function
Major sperm protein (MSP) domain / MSP (Major sperm protein) domain / Major sperm protein (MSP) domain profile. / PapD-like superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Major sperm protein isoform beta
Similarity search - Component
Biological speciesAscaris suum (pig roundworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, SINGLE ISOMORPHOUS REPLACEMENT / Resolution: 3.3 Å
AuthorsBullock, T.L. / Mccoy, A.J. / Stewart, M.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: Structural basis for amoeboid motility in nematode sperm.
Authors: Bullock, T.L. / McCoy, A.J. / Kent, H.M. / Roberts, T.M. / Stewart, M.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: 2.5 A Resolution Crystal Structure of the Motile Major Sperm Protein (Msp) of Ascaris Suum
Authors: Bullock, T.L. / Roberts, T.M. / Stewart, M.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: Worm Sperm and Advances in Cell Locomotion
Authors: Theriot, J.A.
#3: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization of the Motile Major Sperm Protein (Msp) of the Nematode Ascaris Suum
Authors: Stewart, M. / King, K.L. / Roberts, T.M.
History
DepositionDec 19, 1997Processing site: BNL
Revision 1.0Apr 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MAJOR SPERM PROTEIN
B: MAJOR SPERM PROTEIN
C: MAJOR SPERM PROTEIN
D: MAJOR SPERM PROTEIN
E: MAJOR SPERM PROTEIN
F: MAJOR SPERM PROTEIN
G: MAJOR SPERM PROTEIN
H: MAJOR SPERM PROTEIN


Theoretical massNumber of molelcules
Total (without water)112,9678
Polymers112,9678
Non-polymers00
Water0
1
A: MAJOR SPERM PROTEIN
B: MAJOR SPERM PROTEIN
C: MAJOR SPERM PROTEIN
D: MAJOR SPERM PROTEIN


Theoretical massNumber of molelcules
Total (without water)56,4844
Polymers56,4844
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: MAJOR SPERM PROTEIN
F: MAJOR SPERM PROTEIN
G: MAJOR SPERM PROTEIN
H: MAJOR SPERM PROTEIN


Theoretical massNumber of molelcules
Total (without water)56,4844
Polymers56,4844
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.660, 79.660, 463.790
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 / / MSP


Mass: 14120.876 Da / Num. of mol.: 8 / Mutation: C59S, T90C
Source method: isolated from a genetically manipulated source
Details: BETA ISOFORM / Source: (gene. exp.) Ascaris suum (pig roundworm) / Strain: BL21 (DE3) / Cell: SPERM CELL / Cell line: BL21 / Gene: BETA MSP C59S/T90C / Plasmid: PET11D / Species (production host): Escherichia coli / Gene (production host): BETA MSP C59S/T90C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P27440

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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: 3.25 Å3/Da / Density % sol: 62.21 %
Crystal growpH: 8.5
Details: PROTEIN WAS CRYSTALLIZED FROM 16% PEG 6000, 80MM AMMONIUM SULFATE, 100MM TRIS - HCL, PH 8.5
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
240 mMammonium sulfate1drop
35 mMTris-HCl1drop
41 mMdithiothreitol1drop
516 %PEG60001reservoir
680 mMammonium sulfate1reservoir
7100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1997 / Details: OPTICS
RadiationMonochromator: MONOCHROMATOR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 23854 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 5.7
Reflection
*PLUS
Num. measured all: 279016

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Processing

Software
NameVersionClassification
AMoREphasing
MLPHAREphasing
SOLOMONphasing
TNT5Drefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, SINGLE ISOMORPHOUS REPLACEMENT
Starting model: PDB ENTRY 1MSP

1msp


Resolution: 3.3→10 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1183 5 %RANDOM
Rwork0.218 ---
all0.22 23060 --
obs0.22 23060 100 %-
Solvent computationSolvent model: DEFAULT METHOD OF TNT / Bsol: 294 Å2 / ksol: 0.05 e/Å3
Refinement stepCycle: LAST / Resolution: 3.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7824 0 0 0 7824
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.02180080.02
X-RAY DIFFRACTIONt_angle_deg2108003
X-RAY DIFFRACTIONt_dihedral_angle_d21.9
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.01711520.02
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.03530210
Software
*PLUS
Name: TNT / Version: 5D / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.263
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg21.9
X-RAY DIFFRACTIONt_chiral_restr0.0170.02

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