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- PDB-3nom: Crystal Structure of Zymomonas mobilis Glutaminyl Cyclase (monocl... -

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Basic information

Entry
Database: PDB / ID: 3nom
TitleCrystal Structure of Zymomonas mobilis Glutaminyl Cyclase (monoclinic form)
ComponentsGlutamine cyclotransferase
KeywordsTRANSFERASE / beta-propeller / glutaminyl cyclase / CYCLOTRANSFERASE / pyroglutamate
Function / homologyGlutaminyl-peptide cyclotransferase / Glutamine cyclotransferase / glutaminyl-peptide cyclotransferase activity / Quinoprotein amine dehydrogenase, beta chain-like / WD40/YVTN repeat-like-containing domain superfamily / membrane / metal ion binding / Glutamine cyclotransferase / :
Function and homology information
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsParthier, C. / Carrillo, D.R. / Stubbs, M.T.
CitationJournal: Biol.Chem. / Year: 2010
Title: Kinetic and structural characterization of bacterial glutaminyl cyclases from Zymomonas mobilis and Myxococcus xanthus
Authors: Carrillo, D.R. / Parthier, C. / Janckel, N. / Grandke, J. / Stelter, M. / Schilling, S. / Boehme, M. / Neumann, P. / Wolf, R. / Demuth, H.U. / Stubbs, M.T. / Rahfeld, J.U.
History
DepositionJun 25, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2014Group: 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_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_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamine cyclotransferase
B: Glutamine cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8457
Polymers59,4812
Non-polymers3645
Water1,964109
1
A: Glutamine cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9694
Polymers29,7401
Non-polymers2283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutamine cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8773
Polymers29,7401
Non-polymers1362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.380, 85.040, 64.860
Angle α, β, γ (deg.)90.000, 108.160, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glutamine cyclotransferase


Mass: 29740.471 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Strain: subsp. mobilis ATCC 10988, DSMZ 424 / Gene: ZmobDRAFT_1643 / Plasmid: pEt28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: C5TI01, UniProt: A0A0H3G2U5*PLUS, glutaminyl-peptide cyclotransferase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.57 Å3/Da / Density % sol: 52.18 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 2, 2007 / Details: confocal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→29 Å / Num. obs: 23164 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 32.953 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 14.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.4-2.50.5560.6283.420022273226330.67496.4
2.5-2.60.4780.54417092230822380.57997
2.6-2.70.4040.4494.814549197319090.48296.8
2.7-2.80.280.3266.412814171816790.34997.7
2.8-3.160.1810.2069.733514449943880.2297.5
3.16-3.520.0850.10817.221509287028190.11698.2
3.52-3.880.0560.07922.214261191318750.08598
3.88-4.240.0430.06327.29962131713060.06899.2
4.24-4.60.0310.04833.870139399240.05298.4
4.6-100.040.05330.223063308830560.05799
10-200.020.03646.522113083050.03999
20-300.0150.03639.521234320.03994.1
3015

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å24.72 Å
Translation2.5 Å24.72 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER1.3.3phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IWA

2iwa


Resolution: 2.4→28.98 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.891 / WRfactor Rfree: 0.2323 / WRfactor Rwork: 0.1754 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7891 / SU B: 8.727 / SU ML: 0.201 / SU R Cruickshank DPI: 0.384 / SU Rfree: 0.2766 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2682 1158 5 %RANDOM
Rwork0.1994 ---
obs0.2029 23145 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.83 Å2 / Biso mean: 26.0348 Å2 / Biso min: 2.15 Å2
Baniso -1Baniso -2Baniso -3
1-3.54 Å20 Å20.63 Å2
2---1.93 Å20 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 2.4→28.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3794 0 18 109 3921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223911
X-RAY DIFFRACTIONr_angle_refined_deg1.8291.9425319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.055466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54323.958192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.19415642
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8051524
X-RAY DIFFRACTIONr_chiral_restr0.110.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213002
X-RAY DIFFRACTIONr_mcbond_it0.9091.52314
X-RAY DIFFRACTIONr_mcangle_it1.69723760
X-RAY DIFFRACTIONr_scbond_it2.59531597
X-RAY DIFFRACTIONr_scangle_it4.0694.51559
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 84 -
Rwork0.267 1588 -
all-1672 -
obs--100 %

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