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- PDB-3iev: Crystal Structure of ERA in Complex with MgGNP and the 3' End of ... -

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Basic information

Entry
Database: PDB / ID: 3iev
TitleCrystal Structure of ERA in Complex with MgGNP and the 3' End of 16S rRNA
Components
  • 5'-R(P*AP*UP*CP*AP*CP*CP*UP*CP*CP*UP*UP*A)-3'
  • GTP-binding protein era
KeywordsNucleotide binding protein/RNA / ERA / GTPase / KH domain / anti-SD / 16S rRNA / 30S ribosome assembly / GTP-binding / Nucleotide-binding / RNA-binding / Nucleotide binding protein-RNA COMPLEX
Function / homology
Function and homology information


ribosomal small subunit binding / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / rRNA binding / GTPase activity / GTP binding / plasma membrane / cytosol
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 / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 ...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 / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / K homology domain superfamily, prokaryotic type / 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / RNA / RNA (> 10) / GTPase Era
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTu, C. / Ji, X.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structure of ERA in complex with the 3' end of 16S rRNA: implications for ribosome biogenesis
Authors: Tu, C. / Zhou, X. / Tropea, J.E. / Austin, B.P. / Waugh, D.S. / Court, D.L. / Ji, X.
History
DepositionJul 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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 / _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.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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTP-binding protein era
D: 5'-R(P*AP*UP*CP*AP*CP*CP*UP*CP*CP*UP*UP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1585
Polymers38,5152
Non-polymers6433
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-28 kcal/mol
Surface area15210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.600, 71.600, 43.600
Angle α, β, γ (deg.)90.00, 101.50, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-477-

HOH

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Components

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Protein / RNA chain , 2 types, 2 molecules AD

#1: Protein GTP-binding protein era


Mass: 34822.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: genomic DNA / Gene: aq_1994, era, era1 / Plasmid: pBA1971 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O67800
#2: RNA chain 5'-R(P*AP*UP*CP*AP*CP*CP*UP*CP*CP*UP*UP*A)-3'


Mass: 3693.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The RNA has been commercially synthesized.

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Non-polymers , 4 types, 248 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.37 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M (NH4)2SO4, 0.1 M Cacodylate and 30% PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 21, 2008 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 27880 / % possible obs: 98.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 15.3
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.501 / % possible all: 91

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.4.0057refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WF3

1wf3


Resolution: 1.9→23.72 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.555 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22747 1428 5.1 %RANDOM
Rwork0.18321 ---
obs0.18546 26655 98.51 %-
all-27880 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.738 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20.17 Å2
2--0.34 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.9→23.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2395 224 38 245 2902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222869
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1112.133974
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7975336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.84324.28698
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79215519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2481518
X-RAY DIFFRACTIONr_chiral_restr0.070.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211985
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.3811.51569
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.72722599
X-RAY DIFFRACTIONr_scbond_it1.12231300
X-RAY DIFFRACTIONr_scangle_it1.8614.51357
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 84 -
Rwork0.271 1787 -
obs--89.31 %
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)
11.22790.37930.05581.26670.0263.11950.0119-0.1148-0.02990.1244-0.01920.03670.2268-0.15450.00730.0099-0.028-0.0807-0.22650.0133-0.0596-18.82331.109-4.358
23.14110.10780.08711.592-0.05981.06030.00290.05010.06850.0561-0.0451-0.0678-0.1554-0.01220.04220.0338-0.0021-0.1054-0.25420.0251-0.0499-13.27652.121-21.132
37.3093-3.06230.3214.4960.73290.8625-0.0869-0.11121.0472-0.0610.2641-0.3627-0.25020.1915-0.17720.0149-0.0554-0.0425-0.13290.0980.0947-6.27263.159-24.255
412.5713.510917.94166.82955.402630.7568-0.0404-0.1020.12160.10350.12450.1183-0.5182-0.2613-0.08410.036-0.0193-0.0349-0.1279-0.028-0.0239-14.33341.964-2.208
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 185
2X-RAY DIFFRACTION2A186 - 301
3X-RAY DIFFRACTION3D1 - 30
4X-RAY DIFFRACTION4C1 - 1000

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