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- PDB-1wsr: Crystal Structure of Human T-protein of Glycine Cleavage System -

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Basic information

Entry
Database: PDB / ID: 1wsr
TitleCrystal Structure of Human T-protein of Glycine Cleavage System
ComponentsAminomethyltransferase
KeywordsTRANSFERASE / GLYCINE-CLEAVAGE SYTEM / AMINOMETHYL TRANSFERASE
Function / homology
Function and homology information


aminomethyltransferase / glycine catabolic process / aminomethyltransferase activity / Glycine degradation / glycine decarboxylation via glycine cleavage system / transaminase activity / mitochondrial matrix / mitochondrion / nucleoplasm
Similarity search - Function
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 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, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsOkamura-Ikeda, K. / Hosaka, H. / Yoshimura, M. / Yamashita, E. / Toma, S. / Nakagawa, A. / Fujiwara, K. / Motokawa, Y. / Taniguchi, H.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal Structure of Human T-protein of Glycine Cleavage System at 2.0A Resolution and its Implication for Understanding Non-ketotic Hyperglycinemia
Authors: Okamura-Ikeda, K. / Hosaka, H. / Yoshimura, M. / Yamashita, E. / Toma, S. / Nakagawa, A. / Fujiwara, K. / Motokawa, Y. / Taniguchi, H.
History
DepositionNov 10, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2005Provider: 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 / 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: Aminomethyltransferase
B: Aminomethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,91313
Polymers81,8562
Non-polymers1,05711
Water21,2041177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-128 kcal/mol
Surface area30810 Å2
MethodPISA
2
A: Aminomethyltransferase
hetero molecules

B: Aminomethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,91313
Polymers81,8562
Non-polymers1,05711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area2840 Å2
ΔGint-137 kcal/mol
Surface area31700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.170, 128.520, 136.170
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 / GCVT


Mass: 40928.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GCST / Plasmid: pET3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P48728, aminomethyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1177 / 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: 2.9 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: ammonium sulfate, potassium sodium tartrate, citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: May 31, 2003
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→95.3 Å / Num. all: 64914 / Num. obs: 64914 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Biso Wilson estimate: 9 Å2 / Rmerge(I) obs: 0.096
Reflection shellResolution: 2→2.07 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 9.9 / Num. unique all: 6380 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2→49.92 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2538972.03 / 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
Rfree0.193 3281 5.1 %RANDOM
Rwork0.159 ---
obs0.159 64831 99.7 %-
all-64831 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.3929 Å2 / ksol: 0.378175 e/Å3
Displacement parametersBiso mean: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.29 Å20 Å20 Å2
2--2.93 Å20 Å2
3----0.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 2→49.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5656 0 55 1177 6888
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.782
X-RAY DIFFRACTIONc_scbond_it2.282
X-RAY DIFFRACTIONc_scangle_it3.352.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.21 530 5.1 %
Rwork0.168 9872 -
obs--97.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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