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- PDB-1wos: Crystal Structure of T-protein of the Glycine Cleavage System -

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Basic information

Entry
Database: PDB / ID: 1wos
TitleCrystal Structure of T-protein of the Glycine Cleavage System
ComponentsAminomethyltransferase
KeywordsTRANSFERASE / aminomethyltransferase / T-protein
Function / homology
Function and homology information


aminomethyltransferase / aminomethyltransferase activity / glycine decarboxylation via glycine cleavage system / transaminase activity / cytosol
Similarity search - Function
Glycine cleavage system T protein, bacteria / Aminomethyltransferase fragment / Aminomethyltransferase fragment / Glycine cleavage system T protein / Aminomethyltransferase beta-barrel domains / Aminomethyltransferase beta-barrel domains / Glycine cleavage T-protein, C-terminal barrel domain / Glycine cleavage T-protein C-terminal barrel domain / Glycine cleavage T-protein/YgfZ, C-terminal / Probable tRNA modification gtpase trme; domain 1 ...Glycine cleavage system T protein, bacteria / Aminomethyltransferase fragment / Aminomethyltransferase fragment / Glycine cleavage system T protein / Aminomethyltransferase beta-barrel domains / Aminomethyltransferase beta-barrel domains / Glycine cleavage T-protein, C-terminal barrel domain / Glycine cleavage T-protein C-terminal barrel domain / Glycine cleavage T-protein/YgfZ, C-terminal / Probable tRNA modification gtpase trme; domain 1 / Aminomethyltransferase-like / Aminomethyltransferase, folate-binding domain / Aminomethyltransferase folate-binding domain / GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1 / Gyrase A; domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / Few Secondary Structures / Irregular / Alpha-Beta Plaits / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Aminomethyltransferase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Crystal 1 SINGLE WAVELENGTH PROTOCOL, Crysatl 2 MAD PROTOCOL / Resolution: 1.84 Å
AuthorsLee, H.H. / Kim, D.J. / Ahn, H.J. / Ha, J.Y. / Suh, S.W.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal Structure of T-protein of the Glycine Cleavage System: Cofactor binding, insights into H-protein recognition, and molecular basis for understanding nonketotic hyperglycinemia
Authors: Lee, H.H. / Kim, D.J. / Ahn, H.J. / Ha, J.Y. / Suh, S.W.
History
DepositionAug 24, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminomethyltransferase


Theoretical massNumber of molelcules
Total (without water)40,3811
Polymers40,3811
Non-polymers00
Water4,990277
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.365, 53.852, 149.157
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aminomethyltransferase / / Glycine cleavage system T protein


Mass: 40381.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9WY54, aminomethyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / 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

CrystalDensity Matthews: 2.607 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4.25
Details: PEG 3350, sodium dihydrogen phosphate, pH 4.25, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 0.98020, 0.97947, 0.97935, 0.9500
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 23, 2004 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98021
20.979471
30.979351
40.951
ReflectionResolution: 1.84→20 Å / Num. all: 38084 / Num. obs: 37551 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 11.3 Å2
Reflection shellResolution: 1.84→1.91 Å / % possible all: 90

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: Crystal 1 SINGLE WAVELENGTH PROTOCOL, Crysatl 2 MAD PROTOCOL
Resolution: 1.84→19.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 281265.65 / 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
Rfree0.248 3611 10 %RANDOM
Rwork0.218 ---
obs0.218 36270 96.9 %-
all-36270 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.8796 Å2 / ksol: 0.373529 e/Å3
Displacement parametersBiso mean: 19.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.06 Å20 Å20 Å2
2---1.58 Å20 Å2
3----1.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.84→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2810 0 0 277 3087
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.991.5
X-RAY DIFFRACTIONc_mcangle_it2.582
X-RAY DIFFRACTIONc_scbond_it4.272
X-RAY DIFFRACTIONc_scangle_it6.072.5
LS refinement shellResolution: 1.84→1.96 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 504 9.1 %
Rwork0.233 5054 -
obs--90.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAM

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