[English] 日本語
Yorodumi
- PDB-2msp: MAJOR SPERM PROTEIN, BETA ISOFORM, ENGINEERED C59S/T90C MUTANT, P... -

+
Open data


ID or keywords:

Loading...

-
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 / Immunoglobulin-like fold / Immunoglobulins / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more