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- PDB-3vuv: Crystal structure of the merozoite surface protein MSPDBL2 from P... -

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Basic information

Entry
Database: PDB / ID: 3vuv
TitleCrystal structure of the merozoite surface protein MSPDBL2 from P. falciparum bound to zinc
ComponentsErythrocyte membrane protein, putative
KeywordsCELL ADHESION / Duffy Binding-Like domain / Erythrocyte Binding / Merozoite Surface / Malaria
Function / homology
Function and homology information


host cell surface binding / host cell surface receptor binding / cell surface / metal ion binding / membrane
Similarity search - Function
Merozoite surface protein-type / Merozoite surface protein (SPAM) / Duffy-antigen binding / Duffy-antigen binding superfamily / Duffy binding domain
Similarity search - Domain/homology
Duffy binding-like merozoite surface protein 2
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.114 Å
AuthorsCzabotar, P.E. / Hodder, A.N. / Clarke, O.B. / Lin, C.S. / Smith, B.J. / Cowman, A.F.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Insights into Duffy binding-like domains through the crystal structure and function of the merozoite surface protein MSPDBL2 from Plasmodium falciparum
Authors: Hodder, A.N. / Czabotar, P.E. / Uboldi, A.D. / Clarke, O.B. / Lin, C.S. / Healer, J. / Smith, B.J. / Cowman, A.F.
History
DepositionJul 9, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Apr 16, 2014Group: Other
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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_asym_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Erythrocyte membrane protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8225
Polymers39,5601
Non-polymers2624
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.690, 102.070, 38.245
Angle α, β, γ (deg.)90.00, 101.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Erythrocyte membrane protein, putative


Mass: 39560.375 Da / Num. of mol.: 1 / Fragment: DBL domain, UNP residues 127-460
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PF10_0355 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IJ45
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAN ARTEFACT OF THE TEV CLEAVAGE SITE INTRODUCED INTO THE EXPRESSION VECTOR

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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: 1.77 Å3/Da / Density % sol: 30.59 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 20% PEG3350 0.2M sodium thiocyanate, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.2718 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2718 Å / Relative weight: 1
ReflectionResolution: 2.11→37.442 Å / Num. obs: 15702 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.11-2.24195.7
2.24-2.4199.9
2.4-2.59199.9
2.59-2.84199.7
2.84-3.17199.9
3.17-3.66199.7
3.66-4.48199.9
4.48-6.33199.6
6.33-20199.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WAU

2wau


Resolution: 2.114→37.442 Å / SU ML: 0.27 / σ(F): 2.05 / Phase error: 27.21 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflectionSelection details
Rfree0.2327 791 5.04 %Random
Rwork0.1739 ---
obs0.177 15702 99.43 %-
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.114→37.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2293 0 4 69 2366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142435
X-RAY DIFFRACTIONf_angle_d1.0283261
X-RAY DIFFRACTIONf_dihedral_angle_d14.959938
X-RAY DIFFRACTIONf_chiral_restr0.077337
X-RAY DIFFRACTIONf_plane_restr0.004421
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.114-2.24670.35011250.2642243497
2.2467-2.42010.31351560.2182460100
2.4201-2.66360.2631260.19222480100
2.6636-3.04880.28861160.18532511100
3.0488-3.84060.22961230.1642501100
3.8406-37.44810.16871450.14162525100
Refinement TLS params.Method: refined / Origin x: 9.1204 Å / Origin y: 6.3232 Å / Origin z: -1.3605 Å
111213212223313233
T0.0783 Å20.0013 Å2-0.0189 Å2-0.086 Å2-0.0068 Å2--0.0821 Å2
L0.8152 °2-0.2619 °2-0.6262 °2-1.0239 °20.2321 °2--0.4726 °2
S0.0179 Å °0.0418 Å °0.0332 Å °-0.0021 Å °0.0124 Å °-0.0933 Å °-0.0182 Å °0.0138 Å °0.0107 Å °
Refinement TLS groupSelection details: all

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