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- PDB-2bjq: Crystal structure of the nematode sperm cell motility protein MFP2 -

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Basic information

Entry
Database: PDB / ID: 2bjq
TitleCrystal structure of the nematode sperm cell motility protein MFP2
ComponentsMFP2A
KeywordsMOTILITY / ASCARIS / NEMATODE / MSP
Function / homologyCytosolic motility protein / Cytosolic motility protein / MFP2
Function and homology information
Biological speciesASCARIS SUUM (pig roundworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsGrant, R.P. / Buttery, S.M. / Ekman, G.C. / Roberts, T.M. / Stewart, M.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structure of Mfp2 and its Function in Enhancing Msp Polymerization in Ascaris Sperm Amoeboid Motility
Authors: Grant, R.P. / Buttery, S.M. / Ekman, G.C. / Roberts, T.M. / Stewart, M.
History
DepositionFeb 7, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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

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Assembly

Deposited unit
A: MFP2A


Theoretical massNumber of molelcules
Total (without water)38,2351
Polymers38,2351
Non-polymers00
Water8,251458
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.604, 74.202, 108.309
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MFP2A


Mass: 38235.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASCARIS SUUM (pig roundworm) / Description: RECOMBINANT PROTEIN EXPRESSED FROM BACTERIA / Cell: SPERM / Plasmid: PMW172 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): DE3(RIL) / References: UniProt: Q7YXK2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 36.88 %
Crystal growpH: 5.2
Details: PROTEIN WAS CRYSTALLIZED FROM 100 MM NA CITRATE PH 5.2, 28% PEG 4000, 200 MM AMMONIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.379
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 9, 2004 / Details: DUAL SLITS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.379 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 33812 / % possible obs: 95.7 % / Observed criterion σ(I): 4 / Redundancy: 4.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.5
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.4 / % possible all: 85.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.525 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1712 5.1 %RANDOM
Rwork0.189 ---
obs0.191 32059 95.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.36 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å20 Å20 Å2
2--1.45 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2653 0 0 458 3111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222726
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.9553698
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4525339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86224.603126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68715440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4191513
X-RAY DIFFRACTIONr_chiral_restr0.110.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022128
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.21212
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21827
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2326
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9351753
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.784152697
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.0551163
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.013151001
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: 1.75→1.79 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.357 93
Rwork0.301 1852

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