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- PDB-7wez: Crystal structure of RRM domain of Cyclophilin 33-like protein of... -

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Basic information

Entry
Database: PDB / ID: 7wez
TitleCrystal structure of RRM domain of Cyclophilin 33-like protein of Plasmodium falciparum
ComponentsRNA-binding protein, putative
KeywordsRNA BINDING PROTEIN / Nucleic acid-binding protein containing conserved RNA motifs
Function / homology
Function and homology information


peptidyl-prolyl cis-trans isomerase activity / protein folding / RNA binding / metal ion binding
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA-binding protein, putative
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVerma, G. / Bhavesh, N.S.
Funding support1items
OrganizationGrant numberCountry
Other governmentICGEB New Delhi Core fund
CitationJournal: To Be Published
Title: Crystal structure of RRM domain of Cyclophilin 33-like protein of Plasmodium falciparum
Authors: Verma, G. / Bhavesh, N.S.
History
DepositionDec 24, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-binding protein, putative
B: RNA-binding protein, putative
C: RNA-binding protein, putative
D: RNA-binding protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6215
Polymers40,5974
Non-polymers241
Water2,882160
1
A: RNA-binding protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1742
Polymers10,1491
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-6 kcal/mol
Surface area4750 Å2
MethodPISA
2
B: RNA-binding protein, putative


Theoretical massNumber of molelcules
Total (without water)10,1491
Polymers10,1491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4550 Å2
MethodPISA
3
C: RNA-binding protein, putative


Theoretical massNumber of molelcules
Total (without water)10,1491
Polymers10,1491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4560 Å2
MethodPISA
4
D: RNA-binding protein, putative


Theoretical massNumber of molelcules
Total (without water)10,1491
Polymers10,1491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.469, 40.802, 97.387
Angle α, β, γ (deg.)90.00, 115.57, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
RNA-binding protein, putative


Mass: 10149.257 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: PF3D7_1320900 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C0H5C7
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.06 Å3/Da / Density % sol: 40 % / Description: Tetragonal bipyramidal
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M magnesium chloride hexahydrate, 0.1 M Tris hydrochloride pH 8.5 and 30 % (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 27, 2018 / Details: Toroidal Mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.9→45.25 Å / Num. obs: 24799 / % possible obs: 97.4 % / Redundancy: 3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.033 / Rrim(I) all: 0.059 / Net I/σ(I): 14.4
Reflection shellResolution: 1.9→5.166 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 2 / Num. unique obs: 1229 / CC1/2: 0.761 / Rpim(I) all: 0.379 / Rrim(I) all: 0.69 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MDF

3mdf


Resolution: 1.9→45.25 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.924 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27606 1202 4.8 %RANDOM
Rwork0.2229 ---
obs0.22543 23644 97.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.978 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å2-0 Å2-0.8 Å2
2--2.35 Å20 Å2
3----0.54 Å2
Refinement stepCycle: 1 / Resolution: 1.9→45.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2467 0 1 160 2628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132509
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172268
X-RAY DIFFRACTIONr_angle_refined_deg1.561.6373393
X-RAY DIFFRACTIONr_angle_other_deg1.3651.5895169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6485316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24623.662142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.80215395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1661512
X-RAY DIFFRACTIONr_chiral_restr0.0750.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022956
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02612
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1823.5421274
X-RAY DIFFRACTIONr_mcbond_other3.1723.5381273
X-RAY DIFFRACTIONr_mcangle_it4.6515.2821584
X-RAY DIFFRACTIONr_mcangle_other4.6515.2851585
X-RAY DIFFRACTIONr_scbond_it3.543.841235
X-RAY DIFFRACTIONr_scbond_other3.543.841235
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4735.6351809
X-RAY DIFFRACTIONr_long_range_B_refined7.51241.9522716
X-RAY DIFFRACTIONr_long_range_B_other7.46841.7482692
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.904→1.953 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 77 -
Rwork0.292 1766 -
obs--98.66 %

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