[English] 日本語
Yorodumi
- PDB-3nol: Crystal structure of Zymomonas mobilis Glutaminyl Cyclase (trigon... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3nol
TitleCrystal structure of Zymomonas mobilis Glutaminyl Cyclase (trigonal 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: 1.7 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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamine cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0615
Polymers29,7401
Non-polymers3204
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.423, 61.423, 98.800
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-507-

HOH

-
Components

#1: Protein Glutamine cyclotransferase / Glutaminyl Cyclase


Mass: 29740.471 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.81 Å3/Da / Density % sol: 32.01 % / Mosaicity: 1.24 °

-
Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 25, 2007 / Details: confocal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→53.225 Å / Num. all: 24365 / Num. obs: 24365 / % possible obs: 99.9 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 21
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.7-1.7980.5740.5361.42797535100.2010.5740.5363.5100
1.79-1.98.30.3520.332.32759433210.1210.3520.336.2100
1.9-2.038.40.2330.2193.42617231060.0790.2330.21910.1100
2.03-2.198.50.1520.1435.12504329460.0520.1520.14315.8100
2.19-2.48.50.1120.10572275926680.0380.1120.10520.4100
2.4-2.698.60.0820.0779.42119824630.0280.0820.07725.8100
2.69-3.18.70.0590.05512.21875621660.020.0590.05534.1100
3.1-3.88.60.0460.04314.91615418730.0150.0460.04345.6100
3.8-5.388.50.0380.03615.71250614730.0130.0380.03654.2100
5.38-22.4628.20.0420.0412.268428390.0150.0420.0452.198.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å22.46 Å
Translation2.5 Å22.46 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASER1.3.3phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IWA

2iwa


Resolution: 1.7→22.46 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.2067 / WRfactor Rwork: 0.169 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8726 / SU B: 2.095 / SU ML: 0.071 / SU R Cruickshank DPI: 0.1206 / SU Rfree: 0.1176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 1241 5.1 %RANDOM
Rwork0.1777 ---
obs0.1798 24339 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 44.8 Å2 / Biso mean: 11.9369 Å2 / Biso min: 4.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.11 Å20 Å2
2--0.23 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.7→22.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1897 0 18 261 2176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221989
X-RAY DIFFRACTIONr_angle_refined_deg1.3951.9442708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9365239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26924.08298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.92115324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.661512
X-RAY DIFFRACTIONr_chiral_restr0.090.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021533
X-RAY DIFFRACTIONr_nbd_refined0.1930.2887
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21336
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2205
X-RAY DIFFRACTIONr_metal_ion_refined0.0790.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.228
X-RAY DIFFRACTIONr_mcbond_it0.7431.51212
X-RAY DIFFRACTIONr_mcangle_it1.1721914
X-RAY DIFFRACTIONr_scbond_it1.8953913
X-RAY DIFFRACTIONr_scangle_it2.8784.5794
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.486 78 -
Rwork0.357 1701 -
all-1779 -
obs--100 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more