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- PDB-3auf: Crystal structure of glycinamide ribonucleotide transformylase 1 ... -

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Basic information

Entry
Database: PDB / ID: 3auf
TitleCrystal structure of glycinamide ribonucleotide transformylase 1 from Symbiobacterium toebii
ComponentsGlycinamide ribonucleotide transformylase 1
KeywordsTRANSFERASE / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Rossmann fold / transformylase / folate binding
Function / homology
Function and homology information


phosphoribosylglycinamide formyltransferase 1 / phosphoribosylglycinamide formyltransferase activity / 'de novo' IMP biosynthetic process
Similarity search - Function
Phosphoribosylglycinamide formyltransferase / Formyl transferase, N-terminal domain / Phosphoribosylglycinamide formyltransferase, active site / Phosphoribosylglycinamide formyltransferase active site. / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoribosylglycinamide formyltransferase
Similarity search - Component
Biological speciesSymbiobacterium toebii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsKanagawa, M. / Baba, S. / Nagira, T. / Kuramitsu, S. / Yokoyama, S. / Sampei, G. / Kawai, G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biochem. / Year: 2013
Title: Structures and reaction mechanisms of the two related enzymes, PurN and PurU.
Authors: Sampei, G. / Kanagawa, M. / Baba, S. / Shimasaki, T. / Taka, H. / Mitsui, S. / Fujiwara, S. / Yanagida, Y. / Kusano, M. / Suzuki, S. / Terao, K. / Kawai, H. / Fukai, Y. / Nakagawa, N. / ...Authors: Sampei, G. / Kanagawa, M. / Baba, S. / Shimasaki, T. / Taka, H. / Mitsui, S. / Fujiwara, S. / Yanagida, Y. / Kusano, M. / Suzuki, S. / Terao, K. / Kawai, H. / Fukai, Y. / Nakagawa, N. / Ebihara, A. / Kuramitsu, S. / Yokoyama, S. / Kawai, G.
History
DepositionFeb 3, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycinamide ribonucleotide transformylase 1


Theoretical massNumber of molelcules
Total (without water)25,0461
Polymers25,0461
Non-polymers00
Water1,63991
1
A: Glycinamide ribonucleotide transformylase 1

A: Glycinamide ribonucleotide transformylase 1


Theoretical massNumber of molelcules
Total (without water)50,0922
Polymers50,0922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area1850 Å2
ΔGint-11 kcal/mol
Surface area19380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.316, 85.316, 58.019
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Glycinamide ribonucleotide transformylase 1 / Phosphoribosylglycinamide formyltransferase


Mass: 25045.764 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Symbiobacterium toebii (bacteria) / Gene: PurN / Plasmid: pET-HisTEV / Production host: Escherichia coli (E. coli) / References: UniProt: E5RXD0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.43 Å3/Da / Density % sol: 49.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.7M Magnesium Formate, 0.1M Sodium Acetate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 29, 2007 / Details: Toroidal Mirror
RadiationMonochromator: Fixed exit Si 111 double crystal monochromater
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 28757 / % possible obs: 100 % / Redundancy: 5.5 % / Biso Wilson estimate: 6.6 Å2 / Rmerge(I) obs: 0.067
Reflection shellResolution: 2.07→2.14 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.213 / Num. unique all: 2888 / % possible all: 100

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Processing

Software
NameVersionClassification
BSSdata collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JKX

1jkx


Resolution: 2.07→45.63 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1539530.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1533 10.1 %RANDOM
Rwork0.209 ---
obs0.209 15142 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.3822 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 17.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å20 Å20 Å2
2--1.65 Å20 Å2
3----3.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 2.07→45.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1623 0 0 91 1714
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.07→2.2 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.247 247 10.1 %
Rwork0.201 2210 -
obs--98.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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