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- PDB-3jud: Human gamma-glutamylamine cyclotransferase, E82Q mutant -

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Basic information

Entry
Database: PDB / ID: 3jud
TitleHuman gamma-glutamylamine cyclotransferase, E82Q mutant
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 / mutant
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: 0.98 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 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 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: AIG2-like domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5384
Polymers17,3521
Non-polymers1863
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.307, 42.443, 84.764
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: 17351.590 Da / Num. of mol.: 1 / Mutation: E82Q
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.: 3 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 1.88 Å3/Da / Density % sol: 34.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12.5%(w/v) PEG3350, 0.3M ammonium nitrate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.826966 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 29, 2009 / Details: beamline optics
RadiationMonochromator: beamline optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826966 Å / Relative weight: 1
ReflectionResolution: 0.98→37.95 Å / Num. all: 74200 / Num. obs: 74200 / % possible obs: 97.7 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 6.7 % / Biso Wilson estimate: 5 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 10.4
Reflection shellResolution: 0.98→1.03 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 2.5 / Num. unique all: 10958 / Rsym value: 0.688 / % possible all: 100

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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: 0.98→27.57 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.722 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17969 3736 5 %RANDOM
Rwork0.15349 ---
obs0.15478 70357 97.54 %-
all-70357 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 8.444 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 0.98→27.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1206 0 12 232 1450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0221262
X-RAY DIFFRACTIONr_bond_other_d0.0010.02889
X-RAY DIFFRACTIONr_angle_refined_deg2.3131.971735
X-RAY DIFFRACTIONr_angle_other_deg1.14932140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9765161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.51521.11163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71615191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3181517
X-RAY DIFFRACTIONr_chiral_restr0.1530.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211442
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02289
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_it2.6031.5764
X-RAY DIFFRACTIONr_mcbond_other0.9241.5296
X-RAY DIFFRACTIONr_mcangle_it3.54921229
X-RAY DIFFRACTIONr_scbond_it4.3963498
X-RAY DIFFRACTIONr_scangle_it6.0324.5495
X-RAY DIFFRACTIONr_rigid_bond_restr1.99732151
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 0.98→1.005 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 297 -
Rwork0.239 5158 -
obs--99.73 %

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