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- PDB-2zxh: Structure of Aquifex aeolicus GidA in the form I crystal -

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Basic information

Entry
Database: PDB / ID: 2zxh
TitleStructure of Aquifex aeolicus GidA in the form I crystal
ComponentstRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmG
KeywordsFAD-BINDING PROTEIN / 5-carboxymethylaminomethyluridine / modification / tRNA / wobble uridine / FAD / tRNA modification enzyme
Function / homology
Function and homology information


tRNA wobble uridine modification / tRNA methylation / flavin adenine dinucleotide binding / cytosol
Similarity search - Function
GidA associated domain, C-terminal subdomain / tRNA uridine 5-carboxymethylaminomethyl modification enzyme, C-terminal subdomain / : / : / tRNA modifying enzyme MnmG/GidA C-terminal helical domain / GidA associated domain 3 / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG/GidA / Elongation Factor Tu (Ef-tu); domain 3 - #260 / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG, C-terminal ...GidA associated domain, C-terminal subdomain / tRNA uridine 5-carboxymethylaminomethyl modification enzyme, C-terminal subdomain / : / : / tRNA modifying enzyme MnmG/GidA C-terminal helical domain / GidA associated domain 3 / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG/GidA / Elongation Factor Tu (Ef-tu); domain 3 - #260 / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG, C-terminal / tRNA modifying enzyme MnmG/GidA C-terminal helical bundle / Glucose inhibited division protein A family signature 1. / MnmG-related, conserved site / Glucose inhibited division protein A family signature 2. / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG-related / MnmG, N-terminal domain / Glucose inhibited division protein A / Elongation Factor Tu (Ef-tu); domain 3 / FAD/NAD(P)-binding domain superfamily / DNA polymerase; domain 1 / Arc Repressor Mutant, subunit A / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATE ION / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsNumata, T. / Osawa, T.
CitationJournal: Structure / Year: 2009
Title: Conserved cysteine residues of GidA are essential for biogenesis of 5-carboxymethylaminomethyluridine at tRNA anticodon
Authors: Osawa, T. / Ito, K. / Inanaga, H. / Nureki, O. / Tomita, K. / Numata, T.
History
DepositionDec 24, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 4, 2012Group: Database references
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: tRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmG
B: tRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,5057
Polymers143,6492
Non-polymers1,8565
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-57 kcal/mol
Surface area46020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.638, 213.272, 231.737
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein tRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmG / GidA / Glucose-inhibited division protein A


Mass: 71824.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: aq_761 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: O66962
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4

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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: 4.37 Å3/Da / Density % sol: 71.86 % / Description: The file contains Friedel pairs.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 1.0M sodium/potassium phosphate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.97928 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 21, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 78176 / % possible obs: 99.5 % / Redundancy: 8 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 11.5
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 2.2 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→19.97 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 46244.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: BULK SOLVENT MODEL USED, The file contains Friedel pairs.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 3800 4.9 %RANDOM
Rwork0.242 ---
obs0.242 78176 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: -1.81175 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 71.1 Å2
Baniso -1Baniso -2Baniso -3
1-24.26 Å20 Å20 Å2
2--0.56 Å20 Å2
3----24.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a1.1 Å1.15 Å
Refinement stepCycle: LAST / Resolution: 3.2→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9593 0 121 0 9714
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it4.051.5
X-RAY DIFFRACTIONc_mcangle_it6.442
X-RAY DIFFRACTIONc_scbond_it5.972
X-RAY DIFFRACTIONc_scangle_it8.752.5
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.418 574 4.6 %
Rwork0.429 11795 -
obs--92.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1fad.paramfad.top
X-RAY DIFFRACTION2protein_rep.paramprotein_rep.top
X-RAY DIFFRACTION3ion.paramion.top

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