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- PDB-2cul: Crystal structure of the GidA-related protein from Thermus thermo... -

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Basic information

Entry
Database: PDB / ID: 2cul
TitleCrystal structure of the GidA-related protein from Thermus thermophilus HB8
ComponentsGlucose-inhibited division protein A-related protein, probable oxidoreductase
KeywordsOXIDOREDUCTASE / Rossmann fold / protein-FAD complex / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


tRNA processing / flavin adenine dinucleotide binding
Similarity search - Function
tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG-related / MnmG, N-terminal domain / Glucose inhibited division protein A / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / : / GidA-related protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsIwasaki, W. / Miyatake, H. / Miki, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proteins / Year: 2005
Title: Crystal structure of the small form of glucose-inhibited division protein A from Thermus thermophilus HB8
Authors: Iwasaki, W. / Miyatake, H. / Miki, K.
History
DepositionMay 26, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Assembly

Deposited unit
A: Glucose-inhibited division protein A-related protein, probable oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6412
Polymers25,8561
Non-polymers7861
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.510, 78.510, 66.095
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Glucose-inhibited division protein A-related protein, probable oxidoreductase / GidA-related protein


Mass: 25855.705 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: GenBank: Q5SH33, UniProt: Q5SH33*PLUS
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.345.6
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, sitting drop7.6PEG 4000, magnesium chloride, Tris-HCl, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
2932vapor diffusion, sitting dropmagnesium formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
2901
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL44B211
SYNCHROTRONSPring-8 BL44B221.0080, 1.0086, 1.0200
Detector
TypeIDDetectorDate
MARRESEARCH1CCDNov 1, 2002
MARRESEARCH2CCDNov 1, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111SINGLE WAVELENGTHMx-ray1
2Si 111MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.0081
31.00861
41.021
ReflectionResolution: 1.65→40 Å / Num. obs: 28463 / % possible obs: 99.1 % / Biso Wilson estimate: 14.7 Å2 / Rsym value: 0.041
Reflection shellResolution: 1.65→1.71 Å / Rsym value: 0.113 / % possible all: 91.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.65→29.72 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1517317.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.199 2825 9.9 %RANDOM
Rwork0.18 ---
obs0.18 28439 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.9893 Å2 / ksol: 0.397511 e/Å3
Displacement parametersBiso mean: 14.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20.4 Å20 Å2
2---0.08 Å20 Å2
3---0.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.65→29.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 53 195 2026
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it1.71.5
X-RAY DIFFRACTIONc_mcangle_it2.332
X-RAY DIFFRACTIONc_scbond_it3.322
X-RAY DIFFRACTIONc_scangle_it4.72.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.263 411 9.2 %
Rwork0.217 4047 -
obs--94.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2fad_xplor_paramfad_xplor_top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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