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- PDB-1ega: CRYSTAL STRUCTURE OF A WIDELY CONSERVED GTPASE ERA -

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Basic information

Entry
Database: PDB / ID: 1ega
TitleCRYSTAL STRUCTURE OF A WIDELY CONSERVED GTPASE ERA
ComponentsPROTEIN (GTP-BINDING PROTEIN ERA)
KeywordsHYDROLASE / ERA / GTPASE / RNA-BINDING / RAS-LIKE
Function / homology
Function and homology information


guanosine tetraphosphate binding / ribosomal small subunit binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA binding / protein phosphorylation / GTPase activity / GTP binding / RNA binding ...guanosine tetraphosphate binding / ribosomal small subunit binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA binding / protein phosphorylation / GTPase activity / GTP binding / RNA binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
GTP-binding protein Era / Era-type guanine nucleotide-binding (G) domain / Era-type guanine nucleotide-binding (G) domain profile. / K homology (KH) domain / 50S ribosome-binding GTPase / GTP binding domain / GMP Synthetase; Chain A, domain 3 / K Homology domain, type 2 / KH domain / K homology domain superfamily, prokaryotic type ...GTP-binding protein Era / Era-type guanine nucleotide-binding (G) domain / Era-type guanine nucleotide-binding (G) domain profile. / K homology (KH) domain / 50S ribosome-binding GTPase / GTP binding domain / GMP Synthetase; Chain A, domain 3 / K Homology domain, type 2 / KH domain / K homology domain superfamily, prokaryotic type / Type-2 KH domain profile. / K homology domain-like, alpha/beta / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.4 Å
AuthorsChen, X. / Ji, X.
Citation
Journal: Proc Natl Acad Sci U S A / Year: 1999
Title: Crystal structure of ERA: a GTPase-dependent cell cycle regulator containing an RNA binding motif.
Authors: X Chen / D L Court / X Ji /
Abstract: ERA forms a unique family of GTPase. It is widely conserved and essential in bacteria. ERA functions in cell cycle control by coupling cell division with growth rate. ERA homologues also are found in ...ERA forms a unique family of GTPase. It is widely conserved and essential in bacteria. ERA functions in cell cycle control by coupling cell division with growth rate. ERA homologues also are found in eukaryotes. Here we report the crystal structure of ERA from Escherichia coli. The structure has been determined at 2.4-A resolution. It reveals a two-domain arrangement of the molecule: an N-terminal domain that resembles p21 Ras and a C-terminal domain that is unique. Structure-based topological search of the C domain fails to reveal any meaningful match, although sequence analysis suggests that it contains a KH domain. KH domains are RNA binding motifs that usually occur in tandem repeats and exhibit low sequence similarity except for the well-conserved segment VIGxxGxxIK. We have identified a betaalphaalphabeta fold that contains the VIGxxGxxIK sequence and is shared by the C domain of ERA and the KH domain. We propose that this betaalphaalphabeta fold is the RNA binding motif, the minimum structural requirement for RNA binding. ERA dimerizes in crystal. The dimer formation involves a significantly distorted switch II region, which may shed light on how ERA protein regulates downstream events.
#1: Journal: Mol.Microbiol. / Year: 1998
Title: Cell Cycle Arrest in Era GTPase Mutants: A Potential Growth Rate-Regulated Checkpoint in E. Coli
Authors: Britton, R.A. / Powell, B.S. / Dasgupta, S. / Sun, Q. / Margolin, W. / Lupski, J.R. / Court, D.L.
History
DepositionDec 1, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 12, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PROTEIN (GTP-BINDING PROTEIN ERA)
B: PROTEIN (GTP-BINDING PROTEIN ERA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1967
Polymers67,7162
Non-polymers4805
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.790, 67.560, 87.290
Angle α, β, γ (deg.)90.00, 115.82, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.436003, 0.021836, 0.89968), (-0.00621, -0.899924, 0.003681), (0.436031, 0.999755, 0.021255)
Vector: -53.95378, 40.59216, 33.22843)

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Components

#1: Protein PROTEIN (GTP-BINDING PROTEIN ERA)


Mass: 33858.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Cellular location: CYTOPLASM/MEMBRANE / Strain: TAP106 / References: UniProt: P06616
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 3.5 Å3/Da / Density % sol: 65 %
Description: THE STRUCTURE WAS SOLVED BY A COMBINATION OF MIR AND MAD METHODS. MAD DATA SETS, USING HG ANOMALOUS SCATTERING AT WAVELENGTH 1.00870A, 1.00764A, 0.99184A AND 1.00903A, WERE COLLECTED AT ...Description: THE STRUCTURE WAS SOLVED BY A COMBINATION OF MIR AND MAD METHODS. MAD DATA SETS, USING HG ANOMALOUS SCATTERING AT WAVELENGTH 1.00870A, 1.00764A, 0.99184A AND 1.00903A, WERE COLLECTED AT NSLS BEAMLINE X9B WITH MAR345 DETECTOR.
Crystal growpH: 8
Details: PROTEIN 8MG/ML TRIS BUFFER 0.1M, PH 8.0 LITHIUM SULFATE 0.8M SODIUM CHLORIDE 0.8M
Components of the solutions
IDNameCrystal-IDSol-ID
1PROTEIN 8MG/ML11
2TRIS BUFFER 0.1M, PH 8.012
3LITHIUM SULFATE 0.8M12
4SODIUM CHLORIDE 0.8M12
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
250 mMTris-HCl1reservoir
30.8 M1reservoirNaCl
41

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 18, 1998 / Details: BENT MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 35696 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 53.4 Å2 / Rsym value: 0.056 / Net I/σ(I): 31.8
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.49 / % possible all: 99.1
Reflection
*PLUS
Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 99.1 % / Rmerge(I) obs: 0.49

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Processing

Software
NameVersionClassification
PHASESphasing
SHARPphasing
X-PLOR3.85refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.4→8 Å / Rfactor Rfree error: 0.0086 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 4
Details: N-TERMINAL RESIDUES 1-3 FOR BOTH CHAINS, AND C-TERMINAL RESIDUES 296-301 FOR CHAIN A AND RESIDUES 297-301 FOR CHAIN B WERE NOT OBSERVED IN THE ELECTRON DNESITY AND NOT INCLUDED IN THE MODEL; ...Details: N-TERMINAL RESIDUES 1-3 FOR BOTH CHAINS, AND C-TERMINAL RESIDUES 296-301 FOR CHAIN A AND RESIDUES 297-301 FOR CHAIN B WERE NOT OBSERVED IN THE ELECTRON DNESITY AND NOT INCLUDED IN THE MODEL; RESIDUES 224 - 228 IN BOTH CHAINS WERE NOT OBSERVED IN THE ELECTRON DENSITY AND NOT INCLUDED IN THE REFINEMENT, BUT BUILT STEREOCHEMICALLY AND INCLUDED IN THE MODEL; RESTRAINTS BETWEEN THE TWO COPIES OF MOLECULES WERE APPLIED DURING THE INITIAL STAGE OF THE REFINEMENT ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1185 5 %RANDOM
Rwork0.243 ---
obs-28848 82.9 %-
Displacement parametersBiso mean: 49.5 Å2
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4616 0 25 149 4790
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.54
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d29
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.19
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.4→2.5 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.367 108 3.75 %
Rwork0.346 2361 -
obs--56.9 %
Software
*PLUS
Name: X-PLOR / Version: 3.85 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.55
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg29
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.19

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