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- PDB-3jub: Human gamma-glutamylamine cyclotransferase -

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Basic information

Entry
Database: PDB / ID: 3jub
TitleHuman gamma-glutamylamine cyclotransferase
ComponentsAIG2-like domain-containing protein 1
KeywordsTRANSFERASE / cyclotransferase / gamma-glutamylamine cyclotransferase / gamma-glutamyl-epsilon-lysine / Epsilon-(gamma-Glutamyl)-lysine / oxoproline / 5-oxo-L-proline / cyclotransferase fold
Function / homology
Function and homology information


gamma-glutamylamine cyclotransferase / modified amino acid catabolic process / gamma-glutamylaminecyclotransferase activity / extracellular exosome / cytosol
Similarity search - Function
Gamma-glutamylaminecyclotransferase / Gamma-glutamylcyclotransferase, AIG2-like domain / Gamma-glutamyl cyclotransferase, AIG2-like / Gamma-glutamyl cyclotransferase-like / Hypothetical upf0131 protein ytfp / Gamma-glutamyl cyclotransferase-like / Gamma-glutamyl cyclotransferase-like superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Gamma-glutamylaminecyclotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsOakley, A.J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Identification and characterization of {gamma}-glutamylamine cyclotransferase: An enzyme responsible for {gamma}-glutamyl-{epsilon}-lysine catabolism
Authors: Oakley, A.J. / Coggan, M. / Board, P.G.
History
DepositionSep 15, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: AIG2-like domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6636
Polymers17,3531
Non-polymers3105
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.995, 41.940, 84.012
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 AIG2-like domain-containing protein 1 / gamma-glutamylamine cyclotransferase


Mass: 17352.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: A2LD1, GGACT / Plasmid: pHUE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BVM4, EC: 2.3.2.4
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 1.83 Å3/Da / Density % sol: 32.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 17.5%(w/v) PEG3350, 0.3M ammonium nitrate, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.956635 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 25, 2009 / Details: beamline optics
RadiationMonochromator: beamline optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.956635 Å / Relative weight: 1
ReflectionResolution: 1.2→29.68 Å / Num. all: 40593 / Num. obs: 40593 / % possible obs: 99.9 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 6.8 % / Biso Wilson estimate: 8.717 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 22.2
Reflection shellResolution: 1.2→1.26 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 5.2 / Num. unique all: 5782 / % possible all: 99.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VKB

1vkb


Resolution: 1.2→29.68 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.912 / SU ML: 0.019 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14876 2032 5 %RANDOM
Rwork0.12305 ---
obs0.12436 38497 99.93 %-
all-38497 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 8.889 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20 Å2
2--0.45 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.2→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1192 0 20 218 1430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0211257
X-RAY DIFFRACTIONr_bond_other_d0.0080.02877
X-RAY DIFFRACTIONr_angle_refined_deg1.911.9761719
X-RAY DIFFRACTIONr_angle_other_deg1.56532115
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8165158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.80621.61362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79715192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0131516
X-RAY DIFFRACTIONr_chiral_restr0.1320.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211423
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02278
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_it2.9324763
X-RAY DIFFRACTIONr_mcbond_other14293
X-RAY DIFFRACTIONr_mcangle_it3.70361214
X-RAY DIFFRACTIONr_scbond_it4.094494
X-RAY DIFFRACTIONr_scangle_it5.2596495
X-RAY DIFFRACTIONr_rigid_bond_restr1.91832134
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.17 156 -
Rwork0.137 2761 -
obs--99.39 %

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