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- PDB-4z8n: Crystal structure of the erythrocyte-binding domain from Plasmodi... -

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Basic information

Entry
Database: PDB / ID: 4z8n
TitleCrystal structure of the erythrocyte-binding domain from Plasmodium vivax reticulocyte-binding protein 2a (PvRBP2a)
ComponentsReticulocyte-binding protein 2a
KeywordsCELL INVASION / reticulocyte-binding / alpha-helical
Function / homologyNBD94 domain / Nucleotide-Binding Domain 94 of RH / metal ion binding / DI(HYDROXYETHYL)ETHER / Reticulocyte-binding protein 2 (RBP2), like
Function and homology information
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.124 Å
AuthorsGruszczyk, J. / Tham, W.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structurally conserved erythrocyte-binding domain in Plasmodium provides a versatile scaffold for alternate receptor engagement.
Authors: Gruszczyk, J. / Lim, N.T. / Arnott, A. / He, W.Q. / Nguitragool, W. / Roobsoong, W. / Mok, Y.F. / Murphy, J.M. / Smith, K.R. / Lee, S. / Bahlo, M. / Mueller, I. / Barry, A.E. / Tham, W.H.
History
DepositionApr 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 1.3Jan 27, 2016Group: Database references
Revision 1.4Oct 9, 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 / citation / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Reticulocyte-binding protein 2a
B: Reticulocyte-binding protein 2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2037
Polymers68,9722
Non-polymers2305
Water3,513195
1
A: Reticulocyte-binding protein 2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6283
Polymers34,4861
Non-polymers1422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Reticulocyte-binding protein 2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5754
Polymers34,4861
Non-polymers893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-57 kcal/mol
Surface area27120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.790, 93.450, 126.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Reticulocyte-binding protein 2a / RBP2


Mass: 34486.129 Da / Num. of mol.: 2 / Fragment: Erythrocyte-binding domain (UNP residues 160-455)
Source method: isolated from a genetically manipulated source
Details: proteolysed fragment of larger experimental construct
Source: (gene. exp.) Plasmodium vivax (strain Salvador I) (eukaryote)
Strain: Salvador I / Gene: PVX_121920 / Plasmid: pPROEX HTb / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 / References: UniProt: A5JZ09

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Non-polymers , 5 types, 200 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.52 Å3/Da / Density % sol: 51.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25% w/v PEG3350, 100 mM HEPES sodium

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.12→49.76 Å / Num. obs: 40211 / % possible obs: 100 % / Redundancy: 14.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.037 / Net I/σ(I): 13.3 / Num. measured all: 573213 / Scaling rejects: 46
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.12-2.1914.11.9161.84597732560.5380.525100
9.01-49.7612.60.04738.878476210.9990.01399.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOSFLM7.0.9data reduction
Aimless0.2.7data scaling
PHENIX1.9-1692phasing
PHENIX1.9-1692refinement
Coot0.7.2model building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SIRAS / Resolution: 2.124→43.84 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 1031 2.57 %Random selection
Rwork0.2031 39108 --
obs0.2038 40139 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.29 Å2 / Biso mean: 56.7806 Å2 / Biso min: 25.16 Å2
Refinement stepCycle: final / Resolution: 2.124→43.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4739 0 11 195 4945
Biso mean--77.07 51.15 -
Num. residues----582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044838
X-RAY DIFFRACTIONf_angle_d0.7126534
X-RAY DIFFRACTIONf_chiral_restr0.026738
X-RAY DIFFRACTIONf_plane_restr0.004825
X-RAY DIFFRACTIONf_dihedral_angle_d14.2471809
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1241-2.23610.34651430.285854855628
2.2361-2.37620.2761520.252755065658
2.3762-2.55960.25191530.233355165669
2.5596-2.81710.3011320.232855645696
2.8171-3.22470.27831270.218355865713
3.2247-4.06230.21781580.184756145772
4.0623-43.84910.18531660.17758376003
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)
12.26691.8453-0.56656.0565-1.91672.61340.0617-0.23140.17830.31340.04460.36620.068-0.6961-0.12050.283-0.02730.00710.5381-0.02320.3088-7.243160.5744108.8994
24.61914.5459-3.93897.9746-5.37984.93920.3328-0.30740.45920.6834-0.20860.0964-0.46890.0059-0.18490.37710.0834-0.0440.2643-0.08720.43436.715582.2627103.8029
34.45960.2952-0.96677.6821-0.04993.37730.0236-0.4987-0.7260.9522-0.08710.11370.9262-0.83040.18740.432-0.1687-0.08350.5050.13920.3932-7.07943.3545113.8734
43.47263.33694.55444.28724.39725.98270.0426-0.03311.5501-0.1508-0.18550.030.2103-0.07830.12380.6122-0.00370.11020.5943-0.13870.854611.11251.332796.2481
54.69970.2521-1.34075.6591-1.66523.9498-0.1219-0.16290.4843-0.05810.20220.0486-0.36060.0644-0.05920.23360.0083-0.0330.2514-0.0540.440124.051576.168796.8789
65.07953.6897-1.43215.5318-2.47523.48260.2835-0.3841-0.71040.294-0.3356-0.80710.4625-0.08470.11940.3212-0.0409-0.09280.26940.02940.41285.068950.2891108.5028
74.2011.9938-4.87546.2943-4.26198.091-0.13850.41180.0734-0.4864-0.0942-0.0635-0.3278-0.1870.12650.33720.1011-0.03830.31170.00180.532617.851476.407189.2208
86.00121.79431.0757.95040.98456.9698-0.38280.11570.30640.0213-0.0222-0.03740.3366-0.86850.33660.3309-0.01590.09920.4699-0.12160.452527.238447.852875.8938
96.68960.4457-6.10265.0246-3.33218.0388-0.7073-0.24030.401-0.75571.1195-0.4801-0.06271.5158-0.64621.1603-0.30760.15071.0662-0.20270.643213.829429.280269.568
103.24841.53212.35365.77025.16557.76980.18280.1631-0.18160.5821-0.0248-0.03021.0984-0.0135-0.22090.38650.00150.02480.23640.07840.372739.126747.665581.067
118.2445.10665.71634.74115.79357.5795-0.44050.720.0972-0.35450.4103-0.05-0.27590.63110.15320.3899-0.0273-0.04240.29150.12490.359740.289555.723975.3217
121.22130.77170.73431.87030.06711.3527-0.1410.49630.08240.12-0.28810.82841.1822-1.01510.20960.6931-0.47590.10051.2258-0.16910.74038.130841.174872.1973
136.90790.35171.43884.07040.74863.9993-0.03270.02440.3927-0.2858-0.0024-0.4434-0.36380.330.01780.3222-0.01270.07850.22950.02590.458734.036473.625688.3905
142.65572.66240.8865.03972.12413.598-0.22650.297-0.1762-0.34460.1190.17290.3164-0.64830.13220.2972-0.07140.03060.435-0.01980.538620.033955.026280.1699
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 158:235)A158 - 235
2X-RAY DIFFRACTION2(chain A and resid 236:279)A236 - 279
3X-RAY DIFFRACTION3(chain A and resid 280:320)A280 - 320
4X-RAY DIFFRACTION4(chain A and resid 321:327)A321 - 327
5X-RAY DIFFRACTION5(chain A and resid 328:363)A328 - 363
6X-RAY DIFFRACTION6(chain A and resid 364:426)A364 - 426
7X-RAY DIFFRACTION7(chain A and resid 427:456)A427 - 456
8X-RAY DIFFRACTION8(chain B and resid 160:193)B160 - 193
9X-RAY DIFFRACTION9(chain B and resid 194:206)B194 - 206
10X-RAY DIFFRACTION10(chain B and resid 207:247)B207 - 247
11X-RAY DIFFRACTION11(chain B and resid 248:288)B248 - 288
12X-RAY DIFFRACTION12(chain B and resid 289:326)B289 - 326
13X-RAY DIFFRACTION13(chain B and resid 327:370)B327 - 370
14X-RAY DIFFRACTION14(chain B and resid 371:451)B371 - 451

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