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- PDB-7c1o: Crystal structure of Aquifex aeolicus Era Y63A bound to GDP.AlF4- -

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Basic information

Entry
Database: PDB / ID: 7c1o
TitleCrystal structure of Aquifex aeolicus Era Y63A bound to GDP.AlF4-
ComponentsGTPase Era
KeywordsHYDROLASE / HAS-GTPase
Function / homology
Function and homology information


ribosomal small subunit binding / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / 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. / 50S ribosome-binding GTPase / GTP binding domain / K Homology domain, type 2 / KH domain / K homology domain superfamily, prokaryotic type / Type-2 KH domain profile. / K homology domain-like, alpha/beta ...GTP-binding protein Era / Era-type guanine nucleotide-binding (G) domain / Era-type guanine nucleotide-binding (G) domain profile. / 50S ribosome-binding GTPase / GTP binding domain / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / : / DI(HYDROXYETHYL)ETHER / GTPase Era
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.18 Å
AuthorsBatra, S. / Prakash, B.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)DST/INT/JSPS/P-248/2017 India
CitationJournal: To be published
Title: Crystal structure of Aquifex aeolicus Era Y63A bound to GDP.AlF4-
Authors: Batra, S. / Prakash, B.
History
DepositionMay 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: GTPase Era
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5687
Polymers34,7301
Non-polymers8386
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-14 kcal/mol
Surface area12870 Å2
Unit cell
Length a, b, c (Å)36.377, 72.860, 120.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein GTPase Era / GTP-BINDING PROTEIN ERA


Mass: 34729.980 Da / Num. of mol.: 1 / Fragment: GTP binding domain / Mutation: Y63A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: era, era1, aq_1994 / Plasmid: pBA1971 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: O67800

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Non-polymers , 7 types, 100 molecules

#2: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.33 Å3/Da / Density % sol: 47.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 10 mg/ml protein with equal volume of 100 mM Bis-Tris, 200 mM Ammonium acetate, 18 % PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.18→46.52 Å / Num. obs: 17524 / % possible obs: 99.9 % / Redundancy: 7.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.03 / Rrim(I) all: 0.083 / Net I/σ(I): 16.9 / Num. measured all: 135548
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.18-2.247.41.052921312480.6220.4091.1311.898.5
9.75-46.526.10.02415372500.9990.0110.02752.199.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.81 Å46.52 Å
Translation5.81 Å46.52 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimless0.5.21data scaling
PHASER2.8.1phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IEV

3iev


Resolution: 2.18→46.52 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 1746 10 %
Rwork0.205 15722 -
obs0.2081 17468 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.1 Å2 / Biso mean: 51.3725 Å2 / Biso min: 22.58 Å2
Refinement stepCycle: final / Resolution: 2.18→46.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2245 0 48 94 2387
Biso mean--42.95 48.88 -
Num. residues----301
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.18-2.240.33391400.30481267140799
2.24-2.320.28511430.265912831426100
2.32-2.40.27641440.24712831427100
2.4-2.490.29641410.240212741415100
2.49-2.610.32071450.27413151460100
2.61-2.750.30981430.246612861429100
2.75-2.920.30191440.2413021446100
2.92-3.140.27321450.229412991444100
3.14-3.460.2811460.214413131459100
3.46-3.960.24171470.189813281475100
3.96-4.990.17421490.157513381487100
4.99-46.520.18091590.18314341593100
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)
13.6812-0.37920.0414.00240.06230.6923-0.0341-0.10530.11460.20070.0057-0.1308-0.1942-0.03960.00010.25550.0141-0.00720.2656-0.00880.2136-3.34960.3857-12.9985
23.0870.99590.17932.7657-0.24790.751-0.08020.1841-0.5651-0.13830.07560.17420.1589-0.1466-0.00010.26950.02060.01190.2994-0.00930.3946-10.2423-13.3807-16.946
30.94190.3907-0.20593.0413-0.35981.7671-0.0826-0.18690.20340.57240.1509-0.1179-0.5858-0.13320.01240.5070.08280.02940.3919-0.0490.308-6.438912.6092-10.8132
41.2634-0.43460.4792.3864-0.37921.7081-0.0068-0.10070.04550.37390.02730.1473-0.8060.01020.00450.55540.07170.02070.36850.03710.3491-7.503319.5041-15.7394
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 85 )A1 - 85
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 161 )A86 - 161
3X-RAY DIFFRACTION3chain 'A' and (resid 162 through 250 )A162 - 250
4X-RAY DIFFRACTION4chain 'A' and (resid 251 through 301 )A251 - 301

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