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- PDB-3av3: Crystal structure of glycinamide ribonucleotide transformylase 1 ... -

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Basic information

Entry
Database: PDB / ID: 3av3
TitleCrystal structure of glycinamide ribonucleotide transformylase 1 from Geobacillus kaustophilus
ComponentsPhosphoribosylglycinamide formyltransferase
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 speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsKanagawa, M. / Baba, S. / Nakagawa, N. / Ebihara, A. / 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 18, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoribosylglycinamide formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5183
Polymers23,4691
Non-polymers492
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.861, 117.408, 67.251
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-241-

HOH

21A-243-

HOH

31A-254-

HOH

41A-259-

HOH

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Components

#1: Protein Phosphoribosylglycinamide formyltransferase /


Mass: 23469.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Gene: GK0266 / Plasmid: pET-HisTEV / Production host: Escherichia coli (E. coli)
References: UniProt: Q5L3C9, phosphoribosylglycinamide formyltransferase 1
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.18 Å3/Da / Density % sol: 43.6 % / Description: The file contains Friedel pairs.
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.4
Details: Bis-Tris 0.1M pH 6.4, 0.5M Sodium Fluoride, PEG 3350 25%, Mg Chloride 0.1M, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97944, 0.90000, 0.97984
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Feb 15, 2008 / Details: Toroidal Mirror
RadiationMonochromator: Fixed exit Si 111 double crystal monochromater
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979441
20.91
30.979841
ReflectionResolution: 1.7→50 Å / Num. obs: 43718 / % possible obs: 99.7 % / Redundancy: 7 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.045
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.115 / Mean I/σ(I) obs: 14.7 / % possible all: 98.6

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Processing

Software
NameVersionClassification
BSSdata collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.7→38.77 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 237504.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: The file contains Friedel pairs. BULK SOLVENT MODEL USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 4249 9.8 %RANDOM
Rwork0.195 ---
obs0.195 43240 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.4148 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 19.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å20 Å20 Å2
2---3.4 Å20 Å2
3---1.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.03 Å
Refinement stepCycle: LAST / Resolution: 1.7→38.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1442 0 2 275 1719
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
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_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
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: 1.7→1.81 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.26 640 9 %
Rwork0.205 6440 -
obs--97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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