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- PDB-5ewp: ARO (armadillo repeats only protein) from Plasmodium falciparum -

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Basic information

Entry
Database: PDB / ID: 5ewp
TitleARO (armadillo repeats only protein) from Plasmodium falciparum
ComponentsARO (armadillo repeats only protein)
KeywordsPROTEIN BINDING / translocation and attachment of rhoptries to apical pole of parasite / armadillo repeats only
Function / homologyLeucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha / Armadillo-domain containing rhoptry protein
Function and homology information
Biological speciesPlasmodium falciparum Santa Lucia (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsBrown, C. / Zhang, K. / Emery, J. / Prusty, D. / Wetzel, J. / Heincke, D. / Gilberger, T. / Junop, M.
CitationJournal: To Be Published
Title: ARO (armadillo repeats only protein) from Plasmodium falciparum
Authors: Brown, C. / Zhang, K. / Emery, J. / Prusty, D. / Wetzel, J. / Heincke, D. / Gilberger, T. / Junop, M.
History
DepositionNov 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.type / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ARO (armadillo repeats only protein)
B: ARO (armadillo repeats only protein)


Theoretical massNumber of molelcules
Total (without water)56,5002
Polymers56,5002
Non-polymers00
Water11,494638
1
A: ARO (armadillo repeats only protein)


Theoretical massNumber of molelcules
Total (without water)28,2501
Polymers28,2501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ARO (armadillo repeats only protein)


Theoretical massNumber of molelcules
Total (without water)28,2501
Polymers28,2501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.800, 54.940, 64.650
Angle α, β, γ (deg.)106.68, 100.57, 99.60
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ARO (armadillo repeats only protein)


Mass: 28250.240 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum Santa Lucia (eukaryote)
Gene: PFAG_00718 / Production host: Escherichia coli (E. coli) / References: UniProt: W7FPA1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 638 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M potassium flouride, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9798 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.8→47.36 Å / Num. obs: 96059 / % possible obs: 97.1 % / Redundancy: 1.8 % / Net I/σ(I): 7.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→33.856 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1917 2623 4.94 %Random selection
Rwork0.1693 ---
obs0.1704 53065 97.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→33.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3677 0 0 638 4315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073737
X-RAY DIFFRACTIONf_angle_d1.0335069
X-RAY DIFFRACTIONf_dihedral_angle_d11.7891349
X-RAY DIFFRACTIONf_chiral_restr0.043606
X-RAY DIFFRACTIONf_plane_restr0.005648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.83270.28881360.24312632X-RAY DIFFRACTION95
1.8327-1.8680.24141250.22282627X-RAY DIFFRACTION96
1.868-1.90610.23841260.21092616X-RAY DIFFRACTION96
1.9061-1.94760.26691270.20782671X-RAY DIFFRACTION96
1.9476-1.99290.24111420.19762637X-RAY DIFFRACTION97
1.9929-2.04270.18941350.18092642X-RAY DIFFRACTION96
2.0427-2.09790.21811360.18332621X-RAY DIFFRACTION97
2.0979-2.15960.20781440.17252678X-RAY DIFFRACTION97
2.1596-2.22930.1921590.16642636X-RAY DIFFRACTION97
2.2293-2.3090.21061620.16692615X-RAY DIFFRACTION97
2.309-2.40140.19781330.17032670X-RAY DIFFRACTION97
2.4014-2.51070.22091590.17712674X-RAY DIFFRACTION98
2.5107-2.6430.21111180.17382690X-RAY DIFFRACTION98
2.643-2.80850.1991270.17472677X-RAY DIFFRACTION98
2.8085-3.02520.18581620.1772685X-RAY DIFFRACTION98
3.0252-3.32940.21531230.17052723X-RAY DIFFRACTION99
3.3294-3.81060.15861210.15072690X-RAY DIFFRACTION99
3.8106-4.79880.1441390.13512681X-RAY DIFFRACTION98
4.7988-33.86220.17421490.17162577X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -19.6834 Å / Origin y: -23.8732 Å / Origin z: -59.8227 Å
111213212223313233
T0.0975 Å20.0171 Å20.0098 Å2-0.0677 Å20.0014 Å2--0.1165 Å2
L0.4068 °20.0944 °20.007 °2-0.1128 °2-0.1257 °2--1.4617 °2
S0.0516 Å °-0.0004 Å °-0.018 Å °0.0162 Å °0.051 Å °0.0114 Å °-0.1704 Å °-0.0797 Å °0.0564 Å °
Refinement TLS groupSelection details: all

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