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- PDB-3pb6: Crystal structure of the catalytic domain of human Golgi-resident... -

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Basic information

Entry
Database: PDB / ID: 3pb6
TitleCrystal structure of the catalytic domain of human Golgi-resident glutaminyl cyclase at pH 6.5
ComponentsGlutaminyl-peptide cyclotransferase-like protein
KeywordsTRANSFERASE / alpha/beta protein / alpha/beta-mixed fold / glutaminyl cyclase / Golgi membrane
Function / homology
Function and homology information


peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase activity / Golgi membrane / Golgi apparatus / zinc ion binding / membrane
Similarity search - Function
M28 Zn-Peptidase Glutaminyl Cyclase / Glutaminyl-peptide cyclotransferase-like / Peptidase M28 / Peptidase family M28 / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / Glutaminyl-peptide cyclotransferase-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsHuang, K.F. / Liaw, S.S. / Huang, W.L. / Chia, C.Y. / Lo, Y.C. / Chen, Y.L. / Wang, A.H.J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structures of human Golgi-resident glutaminyl cyclase and its complexes with inhibitors reveal a large loop movement upon inhibitor binding
Authors: Huang, K.F. / Liaw, S.S. / Huang, W.L. / Chia, C.Y. / Lo, Y.C. / Chen, Y.L. / Wang, A.H.J.
History
DepositionOct 20, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Database references
Revision 1.3Nov 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
X: Glutaminyl-peptide cyclotransferase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2713
Polymers37,0691
Non-polymers2022
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.097, 68.527, 77.348
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 Glutaminyl-peptide cyclotransferase-like protein / Golgi-resident glutaminyl cyclase


Mass: 37068.727 Da / Num. of mol.: 1 / Fragment: Golgi-luminal catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET 32a / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NXS2, glutaminyl-peptide cyclotransferase
#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 1.9 Å3/Da / Density % sol: 35.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50%(v/v) PEG 200, 0.2M MgCl2, 0.1M cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.82653 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 9, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82653 Å / Relative weight: 1
ReflectionResolution: 1.05→30 Å / Num. obs: 127164 / % possible obs: 96.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 37.4
Reflection shellResolution: 1.05→1.09 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 3.5 / Num. unique all: 13085 / % possible all: 96.7

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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: 3PB4

3pb4


Resolution: 1.05→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.611 / SU ML: 0.014 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.026 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1577 6403 5 %RANDOM
Rwork0.13772 ---
obs0.13875 120575 96.27 %-
all-125247 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.498 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2---0.26 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2474 0 6 356 2836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0222545
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1291.9843482
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg65310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.10122.222108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.57215395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.4311522
X-RAY DIFFRACTIONr_chiral_restr0.1480.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0221953
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_it2.2141.51573
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.21822558
X-RAY DIFFRACTIONr_scbond_it4.6713972
X-RAY DIFFRACTIONr_scangle_it6.6454.5924
X-RAY DIFFRACTIONr_rigid_bond_restr2.44332545
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.197 424 -
Rwork0.171 8855 -
obs-9279 95.97 %

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