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- PDB-1e7z: Crystal structure of the EMAP2/RNA binding domain of the p43 prot... -

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Basic information

Entry
Database: PDB / ID: 1e7z
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 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 / cell-cell signaling / GTPase binding ...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 / cell-cell signaling / GTPase binding / angiogenesis / defense response to virus / tRNA binding / inflammatory response / translation / apoptotic process / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / nucleus / membrane / 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 / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsPasqualato, S. / Kerjan, P. / Renault, L. / Menetrey, J. / Mirande, M. / Cherfils, J.
CitationJournal: Embo J. / Year: 2001
Title: Structure of the Emapii Domain of Human Aminoacyl-tRNA Synthetase Complex Reveals Evolutionary Dimeric 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
DepositionSep 13, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDOTHELIAL-MONOCYTE ACTIVATING POLYPEPTIDE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6993
Polymers19,2971
Non-polymers4012
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)36.141, 53.938, 41.371
Angle α, β, γ (deg.)90.00, 111.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ENDOTHELIAL-MONOCYTE ACTIVATING POLYPEPTIDE II


Mass: 19297.332 Da / Num. of mol.: 1
Fragment: C-TERMINAL DOMAIN/RNA BINDING DOMAIN RESIDUES 147-312
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q12904
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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 growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
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: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 26, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 11716 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 17.3 Å2 / Rsym value: 0.042 / Net I/σ(I): 16.7
Reflection shellResolution: 1.9→1.97 Å / Rsym value: 0.183 / % possible all: 96.5
Reflection
*PLUS
Num. measured all: 119628 / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
% possible obs: 96.5 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 6

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
TRUNCATEdata scaling
CNS1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FL0

1fl0


Resolution: 2.05→28.48 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 7632586.78 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.272 947 10.5 %RANDOM
Rwork0.221 ---
obs0.221 9020 96.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.1208 Å2 / ksol: 0.344836 e/Å3
Displacement parametersBiso mean: 32.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.05→28.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1337 0 2 142 1481
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_d25.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.541.5
X-RAY DIFFRACTIONc_mcangle_it2.52
X-RAY DIFFRACTIONc_scbond_it1.932
X-RAY DIFFRACTIONc_scangle_it2.872.5
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.349 173 11.5 %
Rwork0.296 1331 -
obs--96.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94
LS refinement shell
*PLUS
Rfactor obs: 0.296

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