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- PDB-2bjr: Crystal structure of the nematode sperm cell motility protein MFP2B -

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Basic information

Entry
Database: PDB / ID: 2bjr
TitleCrystal structure of the nematode sperm cell motility protein MFP2B
ComponentsMFP2B
KeywordsMOTILITY / ASCARIS / NEMATODE / MSP
Function / homologyCytosolic motility protein / Cytosolic motility protein / metal ion binding / MFP2b
Function and homology information
Biological speciesASCARIS SUUM (pig roundworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 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 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
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: MFP2B
B: MFP2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8326
Polymers82,5092
Non-polymers3234
Water16,664925
1
A: MFP2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5124
Polymers41,2551
Non-polymers2583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: MFP2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3202
Polymers41,2551
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)87.513, 52.954, 95.542
Angle α, β, γ (deg.)90.00, 99.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MFP2B


Mass: 41254.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASCARIS SUUM (pig roundworm) / Cell: SPERM / Plasmid: PMW172 / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): DE3(RIL) / References: UniProt: Q7YXJ9
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 925 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.37 Å3/Da / Density % sol: 47.8 %
Crystal growpH: 4.5
Details: PROTEIN WAS CRYSTALLIZED FROM 100 MM NA MES PH 4.5, 1.85 M AMMONIUM SULPHATE, 10 MM DTT, 10 MM ERCL3, 40 MM KSCN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 11, 2003 / Details: MIRROR
RadiationMonochromator: SILICON CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→47.14 Å / Num. obs: 74855 / % possible obs: 93 % / Observed criterion σ(I): 4 / Redundancy: 14.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 21
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 3.1 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.127
Stereochemistry target values: MAXIMUM LIKELIHOODWITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 3721 5 %RANDOM
Rwork0.184 ---
obs0.186 71055 93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å2-0.74 Å2
2--0.13 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5636 0 12 925 6573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0215807
X-RAY DIFFRACTIONr_bond_other_d0.0020.025099
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.9447880
X-RAY DIFFRACTIONr_angle_other_deg0.812311916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8845716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0920.2790
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026524
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021188
X-RAY DIFFRACTIONr_nbd_refined0.2070.21008
X-RAY DIFFRACTIONr_nbd_other0.2580.25917
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.23356
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2647
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3040.290
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.320.250
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0441.53562
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.88525700
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.61632245
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1434.52180
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: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.255 299
Rwork0.25 5204

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