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- PDB-5w53: Crystal structure of the erythrocyte-binding domain from Plasmodi... -

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Basic information

Entry
Database: PDB / ID: 5w53
TitleCrystal structure of the erythrocyte-binding domain from Plasmodium vivax reticulocyte-binding protein 2b (PvRBP2b)
ComponentsReticulocyte binding protein 2, putative
KeywordsCELL INVASION / reticulocyte-binding / alpha-helical
Function / homologyNBD94 domain / Nucleotide-Binding Domain 94 of RH / : / THIOCYANATE ION / Reticulocyte binding protein 2, putative
Function and homology information
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsGruszczyk, J. / Tham, W.H.
CitationJournal: Science / Year: 2018
Title: Transferrin receptor 1 is a reticulocyte-specific receptor for Plasmodium vivax.
Authors: Gruszczyk, J. / Kanjee, U. / Chan, L.J. / Menant, S. / Malleret, B. / Lim, N.T.Y. / Schmidt, C.Q. / Mok, Y.F. / Lin, K.M. / Pearson, R.D. / Rangel, G. / Smith, B.J. / Call, M.J. / Weekes, M. ...Authors: Gruszczyk, J. / Kanjee, U. / Chan, L.J. / Menant, S. / Malleret, B. / Lim, N.T.Y. / Schmidt, C.Q. / Mok, Y.F. / Lin, K.M. / Pearson, R.D. / Rangel, G. / Smith, B.J. / Call, M.J. / Weekes, M.P. / Griffin, M.D.W. / Murphy, J.M. / Abraham, J. / Sriprawat, K. / Menezes, M.J. / Ferreira, M.U. / Russell, B. / Renia, L. / Duraisingh, M.T. / Tham, W.H.
History
DepositionJun 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2Oct 4, 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
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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reticulocyte binding protein 2, putative
B: Reticulocyte binding protein 2, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,64315
Polymers73,0402
Non-polymers60313
Water14,844824
1
A: Reticulocyte binding protein 2, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8508
Polymers36,5201
Non-polymers3317
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Reticulocyte binding protein 2, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7927
Polymers36,5201
Non-polymers2736
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.500, 124.200, 65.310
Angle α, β, γ (deg.)90.00, 97.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Reticulocyte binding protein 2, putative


Mass: 36519.789 Da / Num. of mol.: 2 / Fragment: ERYTHROCYTE-BINDING DOMAIN (RESIDUES 169-470)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (strain Salvador I) (eukaryote)
Strain: Salvador I / Gene: PVX_094255 / Plasmid: pPROEX HTb / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SHUFFLE T7 / References: UniProt: A5K736
#2: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CNS
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 824 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% W/V PEG3350, 200 MM POTASSIUM THIOCYANATE, 100 MM BIS-TRIS-HCL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K
PH range: 7.5

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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: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.71→34.87 Å / Num. obs: 100494 / % possible obs: 99.4 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 10
Reflection shellResolution: 1.71→1.74 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.711 / Mean I/σ(I) obs: 1.2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
iMOSFLM1.0.7data reduction
Aimless0.2.7data scaling
PHASERphasing
PHENIX1.9-1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4Z8N

4z8n


Resolution: 1.71→34.17 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.22
RfactorNum. reflection% reflectionSelection details
Rfree0.188 1006 1 %Random selection
Rwork0.168 ---
obs0.168 100440 99.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 35.45 Å2
Refinement stepCycle: LAST / Resolution: 1.71→34.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5100 0 23 824 5947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145212
X-RAY DIFFRACTIONf_angle_d1.3216979
X-RAY DIFFRACTIONf_dihedral_angle_d14.0782016
X-RAY DIFFRACTIONf_chiral_restr0.068744
X-RAY DIFFRACTIONf_plane_restr0.007892
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.80020.3051590.273314026X-RAY DIFFRACTION99
1.8002-1.91290.31531460.236714152X-RAY DIFFRACTION99
1.9129-2.06060.24471450.197314114X-RAY DIFFRACTION99
2.0606-2.26790.19771450.167114183X-RAY DIFFRACTION99
2.2679-2.5960.20281310.164914284X-RAY DIFFRACTION100
2.596-3.27030.18381240.164414315X-RAY DIFFRACTION100
3.2703-34.17640.15061560.147614360X-RAY DIFFRACTION100
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)
12.97451.10442.7013.71172.58624.21870.06440.1303-0.0388-0.1156-0.01050.49110.0508-0.0245-0.02120.16480.03330.02080.21380.0120.211712.730982.31325.3086
24.97292.22742.98066.38372.99945.48740.17130.1532-0.1291-0.3548-0.19690.9916-0.087-0.50790.0740.17670.0676-0.04430.3450.00670.51330.578683.23421.828
33.77092.01452.16183.56752.90035.1605-0.1484-0.31080.24280.181-0.12390.26460.0187-0.22880.21220.36890.01090.0890.2511-0.04270.177822.1836100.248726.1632
43.06252.02931.53186.00543.60954.72410.4653-0.2448-0.21870.6313-0.48870.70830.5049-0.64140.05420.2154-0.01230.02860.30680.02770.41423.572576.31418.8572
54.23933.18780.66344.52441.24694.6271-0.23870.4959-0.1817-0.83970.17620.3736-0.1125-0.03190.10760.40710.0361-0.09020.3279-0.04390.326615.108967.6458-11.1004
66.59622.61124.37495.93862.07745.8915-0.00770.3638-0.3488-0.08180.1447-0.249-0.09990.4103-0.12630.1568-0.00570.04620.19050.0190.186138.107785.892612.5749
73.07192.42262.67434.21972.93714.88930.2118-0.1505-0.09720.5037-0.063-0.22560.02730.0673-0.17050.2252-0.00340.00430.19820.02240.153531.664288.669518.8695
82.31152.84331.78416.67143.12372.78030.13120.1279-0.2102-0.32820.00320.0860.11120.0207-0.12880.23270.0455-0.04260.2188-0.01090.182618.263571.4673-1.8185
93.81162.46185.16926.4232.14697.6222-0.3470.11520.29720.42430.1548-0.3523-0.63940.37790.26970.3865-0.05480.02490.2889-0.00520.23743.0861100.536420.1927
102.48492.10572.04943.34191.72013.79010.02890.0104-0.05020.4712-0.0449-0.1178-0.18710.08240.04580.2630.00180.01160.19440.02980.176122.302654.315219.926
116.88894.77463.14047.06413.22925.15240.3899-0.5418-0.03130.9911-0.3688-0.3737-0.4127-0.07120.03690.6023-0.0644-0.01890.28230.05120.211322.546453.975633.0207
123.34332.51213.83926.58544.63216.29230.17760.0125-0.32210.2968-0.02780.0590.3485-0.2569-0.13990.112-0.01790.03040.27-0.01960.30836.963434.82847.394
131.6212.26292.60934.17363.53154.3732-0.0748-0.16670.17680.0099-0.30750.6633-0.174-0.57240.46230.16650.03340.03510.3419-0.03910.34542.662144.472310.5002
144.7245.41265.11817.38146.31375.97040.4862-0.27180.46610.8033-0.4690.4982-0.5451-0.15290.12390.7143-0.04790.03970.33860.00140.238921.760266.338432.2949
154.8329-1.2706-1.49867.44664.61245.97410.2520.0207-0.27710.39970.032-0.6681-0.0380.3972-0.28710.3419-0.0224-0.10530.26150.05080.321539.261467.238721.3526
160.82871.20841.65334.34392.45523.7962-0.01730.1144-0.122-0.3947-0.0150.0628-0.3590.09430.07460.20550.02870.04030.2765-0.01690.187617.594548.1522-3.9404
171.81152.90261.5077.59813.5392.37080.01240.0984-0.08630.20730.0264-0.2967-0.12610.033-0.07340.18410.0023-0.01040.21090.04220.175330.149161.937814.7535
186.56692.50174.65819.20193.97954.07660.13760.199-0.1736-0.38780.0380.25270.10530.1305-0.23130.17210.02880.0130.2258-0.03430.230811.698731.5168-14.4156
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 168:214)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 215:240)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 241:278)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 279:311)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 312:334)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 335:362)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 363:396)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 397:448)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 449:470)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 168:214)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 215:239)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 240:263)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 264:290)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 291:311)
15X-RAY DIFFRACTION15(CHAIN B AND RESID 312:335)
16X-RAY DIFFRACTION16(CHAIN B AND RESID 336:396)
17X-RAY DIFFRACTION17(CHAIN B AND RESID 397:453)
18X-RAY DIFFRACTION18(CHAIN B AND RESID 454:470)

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