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- PDB-6ipa: C-terminal EMAP II-like domain of p43 refined against twinned data -

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Basic information

Entry
Database: PDB / ID: 6ipa
TitleC-terminal EMAP II-like domain of p43 refined against twinned data
Componentsaminoacyl-tRNA synthetase-interacting multifunctional protein p43
KeywordsRNA BINDING PROTEIN / AIMP1 / EMAPII-LIKE DOMAIN / PLASMODIUM
Function / homology
Function and homology information


ligase activity / tRNA binding
Similarity search - Function
tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Glutathione S-transferase, C-terminal domain superfamily / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
(malaria parasite P. vivax) hypothetical protein / Methionine-tRNA ligase, putative
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsManickam, Y. / Harlos, K. / Gupta, S. / Sharma, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (India)PR6303 India
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Crystal structures of the two domains that constitute the Plasmodium vivax p43 protein.
Authors: Gupta, S. / Chhibber-Goel, J. / Sharma, M. / Parvez, S. / Harlos, K. / Sharma, A. / Yogavel, M.
History
DepositionNov 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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: aminoacyl-tRNA synthetase-interacting multifunctional protein p43
B: aminoacyl-tRNA synthetase-interacting multifunctional protein p43
C: aminoacyl-tRNA synthetase-interacting multifunctional protein p43
D: aminoacyl-tRNA synthetase-interacting multifunctional protein p43


Theoretical massNumber of molelcules
Total (without water)91,4894
Polymers91,4894
Non-polymers00
Water2,594144
1
A: aminoacyl-tRNA synthetase-interacting multifunctional protein p43


Theoretical massNumber of molelcules
Total (without water)22,8721
Polymers22,8721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: aminoacyl-tRNA synthetase-interacting multifunctional protein p43


Theoretical massNumber of molelcules
Total (without water)22,8721
Polymers22,8721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: aminoacyl-tRNA synthetase-interacting multifunctional protein p43


Theoretical massNumber of molelcules
Total (without water)22,8721
Polymers22,8721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: aminoacyl-tRNA synthetase-interacting multifunctional protein p43


Theoretical massNumber of molelcules
Total (without water)22,8721
Polymers22,8721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.170, 146.900, 146.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
aminoacyl-tRNA synthetase-interacting multifunctional protein p43 / Methionine-tRNA ligase / putative / tRNA import protein tRIP / putative


Mass: 22872.205 Da / Num. of mol.: 4 / Fragment: EMAP II -Like Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A1G4HHT8, UniProt: A5K3Y7*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.19 Å3/Da / Density % sol: 43.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02M amino acids, 0.1M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.646
11-H, L, K20.354
ReflectionResolution: 2.47→40.75 Å / Num. obs: 29903 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 1 / Rrim(I) all: 0.181 / Net I/σ(I): 12
Reflection shellResolution: 2.47→2.51 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1455 / CC1/2: 0.5 / Rrim(I) all: 1.892 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
PDB_EXTRACT3.24data extraction
DIALSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZKG

5zkg


Resolution: 2.47→36.73 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.2304 / WRfactor Rwork: 0.1788 / FOM work R set: 0.7389 / SU B: 17.217 / SU ML: 0.187 / SU R Cruickshank DPI: 0.0982 / SU Rfree: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2611 1995 6.7 %RANDOM
Rwork0.2017 ---
obs0.2056 27843 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.7 Å2 / Biso mean: 50.161 Å2 / Biso min: 21.38 Å2
Baniso -1Baniso -2Baniso -3
1--42.59 Å2-0 Å2-0 Å2
2--35.19 Å20 Å2
3---7.39 Å2
Refinement stepCycle: final / Resolution: 2.47→36.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5198 0 0 144 5342
Biso mean---46.78 -
Num. residues----660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195286
X-RAY DIFFRACTIONr_bond_other_d0.0010.025226
X-RAY DIFFRACTIONr_angle_refined_deg1.7831.9897129
X-RAY DIFFRACTIONr_angle_other_deg0.841312110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4725656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.7725.411231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.723151017
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6061523
X-RAY DIFFRACTIONr_chiral_restr0.0960.2812
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215863
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021080
LS refinement shellResolution: 2.47→2.533 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 144 -
Rwork0.263 2001 -
all-2145 -
obs--99.49 %
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)
10.3864-0.02230.43720.8396-0.080.79180.02490.0606-0.0118-0.0193-0.0079-0.01950.02240.0313-0.01690.3154-0.0015-0.01230.2724-0.00920.1054-11.497-15.62620.901
20.0959-0.0839-0.17220.79770.03770.85640.006-0.00030.0024-0.03760.01960.0032-0.072-0.0394-0.02560.32080.00150.0080.26890.00820.1058-6.656-44.40434.132
30.288-0.2118-0.03221.00480.20570.8439-0.0052-0.03680.0180.05550.0338-0.08080.0478-0.0325-0.02860.3127-0.0074-0.01220.27180.01050.0841-2.416-2.49752.441
40.4338-0.1706-0.10231.0048-0.1861.03330.06760.0083-0.0176-0.08690.02990.01460.0675-0.0159-0.09750.3026-0.0061-0.00490.29950.00210.07262.399-15.92881.28
50.1394-0.0253-0.05390.00510.01160.02920.01350.00830.02690.00750.001-0.00580.02480.0234-0.01440.2817-0.0079-0.02240.15030.00120.0075-4.974-14.60948.691
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A241 - 405
2X-RAY DIFFRACTION2B241 - 405
3X-RAY DIFFRACTION3C241 - 405
4X-RAY DIFFRACTION4D241 - 405
5X-RAY DIFFRACTION5A501 - 545
6X-RAY DIFFRACTION5B501 - 518
7X-RAY DIFFRACTION5C501 - 541
8X-RAY DIFFRACTION5D501 - 540

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