[English] 日本語
Yorodumi
- PDB-1msp: MAJOR SPERM PROTEIN, ALPHA ISOFORM (RECOMBINANT), PH 4.6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1msp
TitleMAJOR SPERM PROTEIN, ALPHA ISOFORM (RECOMBINANT), PH 4.6
ComponentsMAJOR SPERM PROTEIN
KeywordsCELL MOTILITY PROTEIN / CYTOSKELETAL PROTEIN / SPERM
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 / Immunoglobulins / Immunoglobulin-like fold / 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 / Resolution: 2.5 Å
AuthorsBullock, T.L. / Roberts, T.M. / Stewart, M.
Citation
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.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: Worm Sperm and Advances in Cell Locomotion
Authors: Theriot, J.A.
#2: Journal: J.Struct.Biol. / Year: 1996
Title: New Crystal Forms of the Motile Major Sperm Protein (Msp) of Ascaris Suum
Authors: Bullock, T.L. / Parthasarathy, G. / King, K.L. / Kent, H.M. / Roberts, T.M. / Stewart, M.
#3: Journal: Curr.Opin.Cell Biol. / Year: 1995
Title: Nematode Sperm Locomotion
Authors: Roberts, T.M. / Stewart, M.
History
DepositionMay 20, 1996Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MAJOR SPERM PROTEIN
B: MAJOR SPERM PROTEIN


Theoretical massNumber of molelcules
Total (without water)28,5562
Polymers28,5562
Non-polymers00
Water1,33374
1
A: MAJOR SPERM PROTEIN
B: MAJOR SPERM PROTEIN

A: MAJOR SPERM PROTEIN
B: MAJOR SPERM PROTEIN


Theoretical massNumber of molelcules
Total (without water)57,1124
Polymers57,1124
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)215.360, 38.480, 32.460
Angle α, β, γ (deg.)90.00, 93.11, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein MAJOR SPERM PROTEIN / / MSP


Mass: 14278.107 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ALPHA ISOFORM, PH 4.6 / Source: (gene. exp.) Ascaris suum (pig roundworm) / Cell: SPERM CELL / Gene: ALPHA MSP / Plasmid: PET11D / Species (production host): Escherichia coli / Gene (production host): ALPHA MSP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27439
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 50 %
Crystal growpH: 4.6 / Details: pH 4.6
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
111 %(w/v)PEG80001reservoir
22 %satammonium sulfate1reservoir
350 mMammonium acetate1reservoir

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 8858 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.046
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 21 Å

-
Processing

Software
NameClassification
TNTrefinement
MOSFLMdata reduction
RefinementResolution: 2.5→20 Å / Num. reflection obs: 8478 / σ(F): 0 / Stereochemistry target values: TNT
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1857 0 0 74 1931
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.0130.02
X-RAY DIFFRACTIONt_angle_deg2.683
X-RAY DIFFRACTIONt_dihedral_angle_d21.8315
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.0110.02
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Lowest resolution: 21 Å / % reflection Rfree: 5 % / Rfactor obs: 0.195 / Rfactor Rfree: 0.292
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg21.8315
X-RAY DIFFRACTIONt_plane_restr0.0110.02

+
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