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

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Basic information

Entry
Database: PDB / ID: 3vuu
TitleCrystal structure of the merozoite surface protein MSPDBL2 from P. falciparum
ComponentsErythrocyte membrane protein, putativeRed blood cell
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 / membrane / metal ion binding
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: 2.093 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Erythrocyte membrane protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0213
Polymers35,9501
Non-polymers712
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.625, 101.499, 38.365
Angle α, β, γ (deg.)90.00, 101.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Erythrocyte membrane protein, putative / Red blood cell


Mass: 35949.598 Da / Num. of mol.: 1 / Fragment: DBL domain, UNP residues 161-460
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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
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: 1.94 Å3/Da / Density % sol: 36.7 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350, 0.2M sodium thiocyanate, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.0163 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 25, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0163 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. all: 16232 / Num. obs: 16184 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.09-2.16197.5
2.16-2.251100
2.25-2.351100
2.35-2.481100
2.48-2.631100
2.63-2.841100
2.84-3.121100
3.12-3.571100
3.57-4.51100
4.5-501100

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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: 2.093→37.583 Å / SU ML: 0.26 / σ(F): 1.91 / Phase error: 28.72 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflectionSelection details
Rfree0.2312 802 5.03 %Random
Rwork0.1826 ---
obs0.1851 16160 99.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.093→37.583 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2248 0 2 52 2302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062303
X-RAY DIFFRACTIONf_angle_d0.9263091
X-RAY DIFFRACTIONf_dihedral_angle_d14.793879
X-RAY DIFFRACTIONf_chiral_restr0.071319
X-RAY DIFFRACTIONf_plane_restr0.004395
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.093-2.1680.31451480.292294295
2.168-2.25470.29831560.26092983100
2.2547-2.35730.29851920.2183012100
2.3573-2.48160.31731770.20932998100
2.4816-2.6370.2531470.20053042100
2.637-2.84060.29211450.19833034100
2.8406-3.12630.27441420.19723047100
3.1263-3.57840.24541370.1773045100
3.5784-4.50720.17671750.15513033100
4.5072-37.58890.1991770.16042998100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.08820.7644-1.03471.6657-0.42121.0564-0.23930.49880.1942-0.39470.3037-0.0199-0.7852-0.1825-0.04090.69460.2614-0.13720.481-0.18480.55153.543211.3766-6.5474
23.2636-2.0573-0.25925.81010.82262.19490.0502-0.07780.67380.17880.0207-0.9383-0.24150.3017-0.08740.2982-0.0887-0.01050.3717-0.06690.45439.679717.91473.3479
33.9704-1.80960.16465.43110.5783.33120.28290.25580.1998-0.365-0.1361-0.1972-0.05460.2167-0.10260.2847-0.00640.02280.27740.00740.28725.067513.3323-1.4977
43.8516-0.69720.73275.7595-0.15434.80470.17930.1602-0.0467-0.4189-0.07480.92860.21-0.5389-0.07570.2957-0.0008-0.06310.3401-0.00110.5298-4.311610.7919-2.5021
55.8733-5.001-4.31474.93933.35523.25940.10140.5353-0.0907-0.2777-0.2103-0.10080.2684-0.08440.12910.49840.0984-0.05390.451-0.07980.40519.7797-7.9397-4.9929
64.2369-1.7035-2.37042.371.37583.9521-0.2858-0.45690.11150.21910.3487-0.15580.77260.5933-0.15860.60490.1671-0.1630.3756-0.06040.452321.7945-8.41993.3645
76.2383-2.2106-2.39442.98431.40042.7761-0.3331-0.6095-0.42490.06020.31790.30370.9509-0.05360.13760.82860.1084-0.13230.4279-0.06270.597715.9472-13.1876-0.3531
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 161 through 194 )
2X-RAY DIFFRACTION2chain A and (resid 195 through 228 )
3X-RAY DIFFRACTION3chain A and (resid 229 through 296 )
4X-RAY DIFFRACTION4chain A and (resid 297 through 344 )
5X-RAY DIFFRACTION5chain A and (resid 345 through 388 )
6X-RAY DIFFRACTION6chain A and (resid 389 through 439 )
7X-RAY DIFFRACTION7chain A and (resid 440 through 457 )

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