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- PDB-1grw: C. elegans major sperm protein -

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Basic information

Entry
Database: PDB / ID: 1grw
TitleC. elegans major sperm protein
ComponentsMAJOR SPERM PROTEIN 31/40/142
KeywordsCYTOSKETAL PROTEIN / CYTOSKELETON / SPERM / CELL MOTILITY
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 19/31/40/45/50/51/53/59/61/65/81/113/142
Similarity search - Component
Biological speciesCAENORHABDITIS ELEGANS (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBaker, A.M.E. / Roberts, T.M. / Stewart, M.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: 2.6 A Resolution Crystal Structure of Helices of the Motile Major Sperm Protein (Msp) of Caenorhabditis Elegans
Authors: Baker, A.M.E. / Roberts, T.M. / Stewart, M.
History
DepositionDec 18, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 2, 2018Group: Advisory / Data collection
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.4Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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

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Assembly

Deposited unit
A: MAJOR SPERM PROTEIN 31/40/142
B: MAJOR SPERM PROTEIN 31/40/142
C: MAJOR SPERM PROTEIN 31/40/142
D: MAJOR SPERM PROTEIN 31/40/142


Theoretical massNumber of molelcules
Total (without water)56,3834
Polymers56,3834
Non-polymers00
Water1,33374
1
A: MAJOR SPERM PROTEIN 31/40/142


Theoretical massNumber of molelcules
Total (without water)14,0961
Polymers14,0961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: MAJOR SPERM PROTEIN 31/40/142


Theoretical massNumber of molelcules
Total (without water)14,0961
Polymers14,0961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: MAJOR SPERM PROTEIN 31/40/142


Theoretical massNumber of molelcules
Total (without water)14,0961
Polymers14,0961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: MAJOR SPERM PROTEIN 31/40/142


Theoretical massNumber of molelcules
Total (without water)14,0961
Polymers14,0961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.478, 53.478, 457.203
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9886, 0.02171, 0.14898), (0.01684, -0.99929, 0.03385), (0.1496, -0.03095, -0.98826)-6.30903, 7.36528, 79.84435
2given(-0.70031, -0.70101, -0.13475), (0.70497, -0.70884, 0.02381), (-0.11221, -0.07832, 0.99059)55.71134, -10.54607, -53.6237
3given(-0.69788, 0.71597, 0.0188), (0.71606, 0.69692, 0.03962), (0.01526, 0.04111, -0.99904)42.52015, -18.15461, 26.02107

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Components

#1: Protein
MAJOR SPERM PROTEIN 31/40/142 / MSP


Mass: 14095.839 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAENORHABDITIS ELEGANS (invertebrata) / Cell: SPERM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P53017
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPROTEIN IS AN IMPORTANT COMPONENT IN THE MOLECULAR INTERACTIONS THAT UNDERLIE SPERM CRAWLING.

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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: 2.9 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5
Details: VAPOUR DIFFUSION AT 20DEGC IN 16% PEG 8000, 100 MM NA ACETATE BUFFER PH5.0, pH 5.00
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
116 %(w/v)PEG80001reservoir
2100 mMsodium acetate1reservoirpH5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Type: ESRF / Wavelength: 0.9311
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9311 Å / Relative weight: 1
ReflectionResolution: 2.43→37.8 Å / Num. obs: 24601 / % possible obs: 98 % / Redundancy: 3.66 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 6.3039
Reflection shellResolution: 2.43→2.56 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1 / % possible all: 87.6
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 38 Å / Num. obs: 21887 / % possible obs: 97.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.74 Å / % possible obs: 97.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
REFMAC4.0.0refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2MSP

2msp


Resolution: 2.6→20 Å / SU B: 10.38 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.507 / ESU R Free: 0.291 / Details: NONE
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1067 4.9 %RANDOM
Rwork0.228 ---
obs-20693 99.62 %-
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3912 0 0 74 3986
Software
*PLUS
Name: REFMAC / Version: '4.0.0 01/12/1999' / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.8

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