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- PDB-1fl0: CRYSTAL STRUCTURE OF THE EMAP2/RNA-BINDING DOMAIN OF THE P43 PROT... -

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Basic information

Entry
Database: PDB / ID: 1fl0
TitleCRYSTAL STRUCTURE OF THE EMAP2/RNA-BINDING DOMAIN OF THE P43 PROTEIN FROM HUMAN AMINOACYL-TRNA SYNTHETASE COMPLEX
ComponentsENDOTHELIAL-MONOCYTE ACTIVATING POLYPEPTIDE II
KeywordsRNA BINDING PROTEIN / RNA-binding domain / OB-fold / tRNA synthetase complex
Function / homology
Function and homology information


positive regulation of glucagon secretion / Selenoamino acid metabolism / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / leukocyte migration / negative regulation of endothelial cell proliferation / Transcriptional and post-translational regulation of MITF-M expression and activity / cytokine activity / GTPase binding / cell-cell signaling ...positive regulation of glucagon secretion / Selenoamino acid metabolism / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / leukocyte migration / negative regulation of endothelial cell proliferation / Transcriptional and post-translational regulation of MITF-M expression and activity / cytokine activity / GTPase binding / cell-cell signaling / angiogenesis / defense response to virus / tRNA binding / inflammatory response / translation / apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / membrane / nucleus / cytosol
Similarity search - Function
: / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Aminoacyl tRNA synthase complex-interacting multifunctional protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.5 Å
AuthorsRenault, L. / Kerjan, P. / Pasqualato, S. / Menetrey, J. / Robinson, J.-C. / Kawaguchi, S. / Vassylyev, D.G. / Yokoyama, S. / Mirande, M. / Cherfils, J.
CitationJournal: EMBO J. / Year: 2001
Title: Structure of the EMAPII domain of human aminoacyl-tRNA synthetase complex reveals evolutionary dimer mimicry.
Authors: Renault, L. / Kerjan, P. / Pasqualato, S. / Menetrey, J. / Robinson, J.C. / Kawaguchi, S. / Vassylyev, D.G. / Yokoyama, S. / Mirande, M. / Cherfils, J.
History
DepositionAug 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 8, 2017Group: Structure summary
Revision 1.4Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDOTHELIAL-MONOCYTE ACTIVATING POLYPEPTIDE II


Theoretical massNumber of molelcules
Total (without water)19,0001
Polymers19,0001
Non-polymers00
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.954, 59.683, 37.850
Angle α, β, γ (deg.)90.00, 114.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ENDOTHELIAL-MONOCYTE ACTIVATING POLYPEPTIDE II


Mass: 18999.955 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN/RNA-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET-28B / Production host: Escherichia coli (E. coli) / References: UniProt: Q12904
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 1.94 Å3/Da / Density % sol: 36.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 35% PEG 3000 or 6000, 100mM TRIS pH7.5, 100-300 mM NaCl, 2mM DTE with a protein concentration of 11 mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
111 mg/mlprotein1drop
228-35 %PEG30001reservoiror PEG6000
3100 mMTris1reservoir
4100-300 mM1reservoirNaCl
52 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 25, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.14→30 Å / Num. obs: 52816 / % possible obs: 93.3 % / Redundancy: 5.1 % / Biso Wilson estimate: 16.5 Å2 / Rsym value: 6.2 / Net I/σ(I): 22.5
Reflection shellResolution: 1.14→1.16 Å / Mean I/σ(I) obs: 6.4 / Rsym value: 15.7 / % possible all: 99.1
Reflection
*PLUS
% possible obs: 99.9 % / Num. measured all: 269210 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 99.1 % / Rmerge(I) obs: 0.157

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Processing

Software
NameVersionClassification
MLPHAREphasing
ARP/wARPmodel building
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 1.5→34.35 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 85632626.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1127 4.8 %RANDOM
Rwork0.221 ---
obs0.221 23301 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.05 Å2 / ksol: 0.318 e/Å3
Displacement parametersBiso mean: 19 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20.94 Å2
2--1.65 Å20 Å2
3----1.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.5→34.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1257 0 0 247 1504
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.581.5
X-RAY DIFFRACTIONc_mcangle_it2.62
X-RAY DIFFRACTIONc_scbond_it2.92
X-RAY DIFFRACTIONc_scangle_it4.62.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 193 5 %
Rwork0.253 3676 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0.1 / % reflection Rfree: 4.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.322 / % reflection Rfree: 5 % / Rfactor Rwork: 0.253 / Rfactor obs: 0.262

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