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- PDB-2zxi: Structure of Aquifex aeolicus GidA in the form II crystal -

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Basic information

Entry
Database: PDB / ID: 2zxi
TitleStructure of Aquifex aeolicus GidA in the form II crystal
ComponentstRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmG
KeywordsFAD-BINDING PROTEIN / modification / tRNA / 5-carboxymethylaminomethyl uridine / 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 / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
C: tRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmG
D: tRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,4398
Polymers287,2974
Non-polymers3,1424
Water19,8171100
1
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)145,2204
Polymers143,6492
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7650 Å2
ΔGint-26 kcal/mol
Surface area47600 Å2
MethodPISA
2
C: tRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmG
D: tRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,2204
Polymers143,6492
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
ΔGint-28 kcal/mol
Surface area47620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.414, 98.001, 129.622
Angle α, β, γ (deg.)90.00, 90.002, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 4
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 / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1100 / 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: 2.64 Å3/Da / Density % sol: 53.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200mM ammonium chloride, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 20, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 123831 / % possible obs: 92.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 12.2
Reflection shellResolution: 2.3→2.33 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 2 / % possible all: 78.5

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZXH

2zxh


Resolution: 2.3→19.92 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3262046.14 / 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
RfactorNum. reflection% reflectionSelection details
Rfree0.248 6095 5 %RANDOM
Rwork0.209 ---
obs0.209 122591 92.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.4801 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 29.5 Å2
Baniso -1Baniso -2Baniso -3
1--6.04 Å20 Å2-0.24 Å2
2---5.97 Å20 Å2
3---12.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19268 0 212 1100 20580
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.751.5
X-RAY DIFFRACTIONc_mcangle_it2.682
X-RAY DIFFRACTIONc_scbond_it3.072
X-RAY DIFFRACTIONc_scangle_it4.372.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.343 889 4.8 %
Rwork0.31 17528 -
obs--83.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1fad.paramfad.top
X-RAY DIFFRACTION2protein_rep.paramprotein_rep.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top

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