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- PDB-1v5v: Crystal Structure of a Component of Glycine Cleavage System: T-pr... -

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Basic information

Entry
Database: PDB / ID: 1v5v
TitleCrystal Structure of a Component of Glycine Cleavage System: T-protein from Pyrococcus horikoshii OT3 at 1.5 A Resolution
Componentsaminomethyltransferase
KeywordsTRANSFERASE / GLYCINE-CLEAVAGE SYTEM / AMINOMETHYL TRANSFERASE / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


aminomethyltransferase / aminomethyltransferase activity / glycine decarboxylation via glycine cleavage system / transaminase activity
Similarity search - Function
Glycine cleavage system T protein, bacteria / 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 ...Glycine cleavage system T protein, bacteria / 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 / Alpha-Beta Plaits / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Probable aminomethyltransferase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsLokanath, N.K. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of a component of glycine cleavage system: T-protein from Pyrococcus horikoshii OT3 at 1.5 A resolution
Authors: Lokanath, N.K. / Kuroishi, C. / Okazaki, N. / Kunishima, N.
History
DepositionNov 26, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 27, 2023Group: 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)92,7565
Polymers92,4662
Non-polymers2903
Water9,854547
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-24 kcal/mol
Surface area31620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.496, 96.099, 118.605
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE BIOLOGICAL ASSEMBLY IS A DIMER GENERATED FROM THE MONOMER USING SYMMETRY OPERATIONS. TWO MOLECULES IN THE ASYMMETRIC UNIT OF THE CRYSTAL FORM AS WELL AS IN SOLUTION

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Components

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


Mass: 46232.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: GCS / Plasmid: PET-11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O58888, aminomethyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 547 / 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: 2.47 Å3/Da / Density % sol: 49.88 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 5.9 / Details: PEG, MES, pH 5.9, MICROBATCH, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 2.0, 0.91971, 0.92001, 0.92540
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 17, 2003
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
121
20.919711
30.920011
40.92541
ReflectionResolution: 1.5→30 Å / Num. all: 141103 / Num. obs: 141020 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.049
Reflection shellResolution: 1.5→1.55 Å / % possible all: 96.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→28.5 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2140110.83 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.209 7136 5.1 %RANDOM
Rwork0.197 ---
obs0.197 141020 97.3 %-
all-141103 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.561 Å2 / ksol: 0.384863 e/Å3
Displacement parametersBiso mean: 18.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--1.81 Å20 Å2
3----1.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→28.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6488 0 19 547 7054
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.85
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.247 1151 5.1 %
Rwork0.232 21560 -
obs--94.8 %

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