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- PDB-3a8k: Crystal Structure of ETD97N-EHred complex -

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Basic information

Entry
Database: PDB / ID: 3a8k
TitleCrystal Structure of ETD97N-EHred complex
Components
  • Aminomethyltransferase
  • Glycine cleavage system H protein
KeywordsTRANSFERASE/TRANSPORT PROTEIN / Glycine Cleavage System / Aminotransferase / Transferase / Lipoyl / TRANSFERASE-TRANSPORT PROTEIN COMPLEX
Function / homology
Function and homology information


aminomethyltransferase / aminomethyltransferase activity / glycine decarboxylation via glycine cleavage system / glycine cleavage complex / transaminase activity / one-carbon metabolic process / cytoplasm / 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 system H-protein, subgroup / Glycine cleavage system H-protein / Glycine cleavage system H-protein/Simiate / Glycine cleavage H-protein ...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 system H-protein, subgroup / Glycine cleavage system H-protein / Glycine cleavage system H-protein/Simiate / Glycine cleavage H-protein / 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 / GCVT N-terminal domain / GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1 / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Gyrase A; domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / Few Secondary Structures / Irregular / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Plaits / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Glycine cleavage system H protein / Aminomethyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsOkamura-Ikeda, K. / Hosaka, H.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structure of aminomethyltransferase in complex with dihydrolipoyl-H-protein of the glycine cleavage system: implications for recognition of lipoyl protein substrate, disease-related ...Title: Crystal structure of aminomethyltransferase in complex with dihydrolipoyl-H-protein of the glycine cleavage system: implications for recognition of lipoyl protein substrate, disease-related mutations, and reaction mechanism
Authors: Okamura-Ikeda, K. / Hosaka, H. / Maita, N. / Fujiwara, K. / Yoshizawa, A.C. / Nakagawa, A. / Taniguchi, H.
History
DepositionOct 6, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 21, 2013Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminomethyltransferase
B: Aminomethyltransferase
C: Aminomethyltransferase
D: Aminomethyltransferase
E: Glycine cleavage system H protein
F: Glycine cleavage system H protein


Theoretical massNumber of molelcules
Total (without water)188,7776
Polymers188,7776
Non-polymers00
Water26,9321495
1
A: Aminomethyltransferase
E: Glycine cleavage system H protein


Theoretical massNumber of molelcules
Total (without water)54,1992
Polymers54,1992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aminomethyltransferase
F: Glycine cleavage system H protein


Theoretical massNumber of molelcules
Total (without water)54,1992
Polymers54,1992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Aminomethyltransferase


Theoretical massNumber of molelcules
Total (without water)40,1901
Polymers40,1901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Aminomethyltransferase


Theoretical massNumber of molelcules
Total (without water)40,1901
Polymers40,1901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.122, 88.412, 97.863
Angle α, β, γ (deg.)91.56, 102.42, 89.59
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Aminomethyltransferase / Glycine cleavage system T protein


Mass: 40189.617 Da / Num. of mol.: 4 / Mutation: D97N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 substr. W3110 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P27248, aminomethyltransferase
#2: Protein Glycine cleavage system H protein


Mass: 14009.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 substr. W3110 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P0A6T9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1495 / 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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 14.4% PEG8000, 0.036M KH2PO4, 18% Glycerol, 0.05M NaCl, 1mM CTAB, 1mM MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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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: Nov 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 119927 / % possible obs: 98.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 20.9
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A8J

3a8j


Resolution: 1.95→43.97 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.621 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22915 6363 5 %RANDOM
Rwork0.17094 ---
obs0.1739 119927 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.512 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.21 Å2-0.87 Å2
2---0.52 Å2-0.06 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.95→43.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13164 0 0 1495 14659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02213475
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8671.95418278
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.60851708
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.07924.2631
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.331152215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1381592
X-RAY DIFFRACTIONr_chiral_restr0.1410.22030
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02110334
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1921.58438
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.971213524
X-RAY DIFFRACTIONr_scbond_it3.22135037
X-RAY DIFFRACTIONr_scangle_it5.0174.54748
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.952→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 464 -
Rwork0.214 8495 -
obs--94.04 %

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