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- PDB-3mbr: Crystal Structure of the Glutaminyl Cyclase from Xanthomonas camp... -

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Basic information

Entry
Database: PDB / ID: 3mbr
TitleCrystal Structure of the Glutaminyl Cyclase from Xanthomonas campestris
ComponentsGlutamine cyclotransferase
KeywordsTRANSFERASE / beta-propeller / cyclotransferase
Function / homologyGlutaminyl-peptide cyclotransferase / Glutamine cyclotransferase / peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase activity / Quinoprotein amine dehydrogenase, beta chain-like / WD40/YVTN repeat-like-containing domain superfamily / metal ion binding / Glutamine cyclotransferase
Function and homology information
Biological speciesXanthomonas campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsHuang, W.-L. / Wang, Y.-R. / Ko, T.-P. / Chia, C.-Y. / Huang, K.-F. / Wang, A.H.-J.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal structure and functional analysis of the glutaminyl cyclase from Xanthomonas campestris
Authors: Huang, W.-L. / Wang, Y.-R. / Ko, T.-P. / Chia, C.-Y. / Huang, K.-F. / Wang, A.H.-J.
History
DepositionMar 25, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2014Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 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
X: Glutamine cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3142
Polymers27,2741
Non-polymers401
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.330, 95.330, 65.088
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11X-355-

HOH

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Components

#1: Protein Glutamine cyclotransferase / glutaminyl cyclase


Mass: 27273.768 Da / Num. of mol.: 1 / Fragment: UNP residues 22-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris (bacteria) / Strain: pv. campestris / Gene: XCC2216 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8P8M4, glutaminyl-peptide cyclotransferase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.68
Details: 50mM imidazole, 0.8M sodium citrate, pH 8.68, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A11
SYNCHROTRONNSRRC BL13B121
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 315r1CCDJun 18, 2009mirrors
ADSC QUANTUM 3152CCD
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.44→30 Å / Num. all: 52562 / Num. obs: 52509 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.034 / Rsym value: 0.034 / Net I/σ(I): 55.1
Reflection shellResolution: 1.44→1.49 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 3.2 / Num. unique all: 5208 / Rsym value: 0.454 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FAW

2faw


Resolution: 1.44→29.31 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.183 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.068 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20871 2669 5.1 %RANDOM
Rwork0.17447 ---
obs0.17625 49776 99.74 %-
all-49906 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.138 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.44→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1881 0 1 259 2141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0221932
X-RAY DIFFRACTIONr_angle_refined_deg2.3011.9532638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0685235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.79822.592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72815301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0021520
X-RAY DIFFRACTIONr_chiral_restr0.1840.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211499
X-RAY DIFFRACTIONr_mcbond_it2.8631.51176
X-RAY DIFFRACTIONr_mcangle_it4.10321903
X-RAY DIFFRACTIONr_scbond_it5.1853756
X-RAY DIFFRACTIONr_scangle_it7.3854.5735
X-RAY DIFFRACTIONr_rigid_bond_restr3.31131932
X-RAY DIFFRACTIONr_sphericity_free8.9313272
X-RAY DIFFRACTIONr_sphericity_bonded7.01931882
LS refinement shellResolution: 1.441→1.479 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 211 -
Rwork0.221 3629 -
obs--99.79 %
Refinement TLS params.Method: refined / Origin x: 71.3023 Å / Origin y: -12.969 Å / Origin z: 37.9908 Å
111213212223313233
T0.0247 Å2-0.0013 Å20.0059 Å2-0.0091 Å20.0026 Å2--0.0363 Å2
L1.7486 °20.2504 °2-0.2167 °2-1.4114 °2-0.192 °2--1.9383 °2
S0.0099 Å °0.0112 Å °-0.0451 Å °0.0008 Å °-0.0136 Å °0.0699 Å °0.0597 Å °-0.1239 Å °0.0037 Å °

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