[English] 日本語
Yorodumi
- PDB-3l9z: Crystal Structure of UreE from Helicobacter pylori (apo form) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3l9z
TitleCrystal Structure of UreE from Helicobacter pylori (apo form)
ComponentsUrease accessory protein ureE
KeywordsMETAL BINDING PROTEIN / UreE apo form (dimer) / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Chaperone / Nickel / Nickel insertion / Virulence
Function / homology
Function and homology information


urea metabolic process / nickel cation binding / unfolded protein binding / protein folding / protein-containing complex assembly / cytoplasm
Similarity search - Function
UreE urease accessory, N-terminal / Urease accessory protein UreE, C-terminal domain / Urease accessory protein UreE / UreE urease accessory, N-terminal domain superfamily / UreE urease accessory protein, N-terminal domain / UreE urease accessory protein, C-terminal domain / UreE urease accessory protein, N-terminal domain / UreE, C-terminal domain / Urease metallochaperone UreE, N-terminal domain / HSP40/DNAj peptide-binding domain ...UreE urease accessory, N-terminal / Urease accessory protein UreE, C-terminal domain / Urease accessory protein UreE / UreE urease accessory, N-terminal domain superfamily / UreE urease accessory protein, N-terminal domain / UreE urease accessory protein, C-terminal domain / UreE urease accessory protein, N-terminal domain / UreE, C-terminal domain / Urease metallochaperone UreE, N-terminal domain / HSP40/DNAj peptide-binding domain / Alpha-Beta Plaits / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Urease accessory protein UreE
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsShi, R. / Munger, C. / Assinas, A. / Matte, A. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Biochemistry / Year: 2010
Title: Crystal Structures of Apo and Metal-Bound Forms of the UreE Protein from Helicobacter pylori: Role of Multiple Metal Binding Sites
Authors: Shi, R. / Munger, C. / Asinas, A. / Benoit, S.L. / Miller, E. / Matte, A. / Maier, R.J. / Cygler, M.
History
DepositionJan 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Urease accessory protein ureE


Theoretical massNumber of molelcules
Total (without water)19,4131
Polymers19,4131
Non-polymers00
Water1,65792
1
A: Urease accessory protein ureE

A: Urease accessory protein ureE


Theoretical massNumber of molelcules
Total (without water)38,8252
Polymers38,8252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area2200 Å2
ΔGint-15 kcal/mol
Surface area15380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.011, 131.011, 51.267
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

-
Components

#1: Protein Urease accessory protein ureE


Mass: 19412.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: ATCC 43504 / Gene: HP_0070, ureE / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q09064
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 3.27 Å3/Da / Density % sol: 62.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 17% PEG 8000, 0.1M Sodium Citrate pH 5.0, vapor diffusion, sitting drop, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.08→42.88 Å / Num. obs: 16040 / % possible obs: 99.8 % / Redundancy: 15.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.08-2.158.10.49699.5
2.15-2.2410.40.41799.7
2.24-2.3413.10.31199.9
2.34-2.4715.40.259100
2.47-2.6215.80.192100
2.62-2.8216.50.125100
2.82-3.1117.50.083100
3.11-3.5619.50.05699.9
3.56-4.4820.60.037100
4.48-5019.10.02598.5

-
Phasing

Phasing MRRfactor: 60.62 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å42.88 Å
Translation2.5 Å42.88 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.2phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→42.88 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.943 / SU ML: 0.113 / SU R Cruickshank DPI: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25488 802 5 %RANDOM
Rwork0.2211 ---
obs0.22277 15182 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.904 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å20.82 Å20 Å2
2--1.65 Å20 Å2
3----2.47 Å2
Refinement stepCycle: LAST / Resolution: 2.08→42.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1170 0 0 92 1262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221203
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.9741625
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8895152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7423.96253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.56615227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.089159
X-RAY DIFFRACTIONr_chiral_restr0.0830.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02882
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.2483
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2811
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.290
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7461.5770
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2621205
X-RAY DIFFRACTIONr_scbond_it1.7693481
X-RAY DIFFRACTIONr_scangle_it2.9794.5418
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.08→2.134 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 65 -
Rwork0.276 1096 -
obs--99.4 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.35380.0345-0.8912.02130.67362.30960.090.0814-0.0096-0.102-0.0144-0.0185-0.0072-0.2056-0.0755-0.01560.00790.0079-0.0190.0173-0.097752.6138-29.5844-4.8332
21.2288-1.65640.72365.5218-1.78551.3666-0.1601-0.03460.07570.45520.0843-0.086-0.1048-0.18620.07580.00640.00510.042-0.0935-0.0108-0.049345.7025-7.616.9873
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 75
2X-RAY DIFFRACTION2A76 - 149

+
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