[English] 日本語
Yorodumi
- PDB-3ux4: Crystal structure of the urea channel from the human gastric path... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ux4
TitleCrystal structure of the urea channel from the human gastric pathogen Helicobacter pylori
ComponentsAcid-activated urea channel
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


identical protein binding / plasma membrane
Similarity search - Function
AmiS/UreI transporter / AmiS/UreI transporter / AmiS/UreI transporter superfamily / AmiS/UreI family transporter / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE / Acid-activated urea channel
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.26 Å
AuthorsMcNulty, R. / Luecke, H.
CitationJournal: Nature / Year: 2012
Title: Structure of the proton-gated urea channel from the gastric pathogen Helicobacter pylori.
Authors: Strugatsky, D. / McNulty, R. / Munson, K. / Chen, C.K. / Soltis, S.M. / Sachs, G. / Luecke, H.
History
DepositionDec 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Mar 6, 2013Group: Structure summary
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Acid-activated urea channel
B: Acid-activated urea channel
C: Acid-activated urea channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,92612
Polymers67,6003
Non-polymers5,3269
Water0
1
A: Acid-activated urea channel
B: Acid-activated urea channel
C: Acid-activated urea channel
hetero molecules

A: Acid-activated urea channel
B: Acid-activated urea channel
C: Acid-activated urea channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,85224
Polymers135,2006
Non-polymers10,65218
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area30100 Å2
ΔGint-128 kcal/mol
Surface area45500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.904, 122.904, 141.348
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
12
13
/ NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.750551, -0.250299, 0.611574), (-0.248946, 0.750203, 0.612554), (-0.612126, -0.612002, 0.500754)0.04967, 0.00615, 0.09779
3given(0.750076, -0.24924, -0.612589), (-0.252691, 0.747985, -0.613731), (0.611174, 0.615141, 0.498065)0.0195, 0.02353, -0.14983
4given(0.251723, -0.749851, -0.611848), (-0.751382, 0.247033, -0.611882), (0.609967, 0.613757, -0.501241)0.1257, 0.17316, -0.13262

-
Components

#1: Protein Acid-activated urea channel / Urease accessory protein UreI


Mass: 22533.258 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: J99 / Gene: jhp_0066, ureI / Plasmid: PET100D / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: P56874
#2: Chemical
ChemComp-XP4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE


Mass: 591.777 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C31H60O8P / Comment: DMPA, phospholipid*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.1 Å3/Da / Density % sol: 69.99 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: Drop: 1.57 mg/mL UreI protein, 0.04 M NaCl, 1 mM TlCl, 0.01 M CaCl2, 7% PEG400, 0.05% decylmaltoside, 2.25% octylglucoside, 0.8 mg/mL E. coli polar lipids, 0.035 M MES, pH5.3, reservoir: 20% ...Details: Drop: 1.57 mg/mL UreI protein, 0.04 M NaCl, 1 mM TlCl, 0.01 M CaCl2, 7% PEG400, 0.05% decylmaltoside, 2.25% octylglucoside, 0.8 mg/mL E. coli polar lipids, 0.035 M MES, pH5.3, reservoir: 20% PEG400, 0.1 M MES, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 285K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 23, 2011
RadiationMonochromator: Kohzu HLD8-24 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 3.256→92.746 Å / Num. all: 17274 / Num. obs: 17263 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.6 / Redundancy: 6.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.2
Reflection shellResolution: 3.256→3.43 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.108 / Mean I/σ(I) obs: 1.6 / % possible all: 97.9

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementResolution: 3.26→39.35 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.888 / SU B: 129.408 / SU ML: 0.853 / Cross valid method: THROUGHOUT / ESU R Free: 0.524 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29949 872 5.1 %RANDOM
Rwork0.23929 ---
obs0.24233 16314 98.18 %-
all-17190 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 164.174 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2---0.63 Å2-0 Å2
3---1.26 Å2
Refinement stepCycle: LAST / Resolution: 3.26→39.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4284 0 198 0 4482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.024629
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.9656312
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7425534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29622.941153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.63715636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.295153
X-RAY DIFFRACTIONr_chiral_restr0.0820.2711
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213333
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr11.15934629
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded54482
Refine LS restraints NCS
Ens-IDDom-IDNumberRefine-IDTypeRms dev position (Å)Weight position
11240X-RAY DIFFRACTIONTIGHT THERMAL46.90.71
21240X-RAY DIFFRACTIONTIGHT THERMAL47.680.71
31240X-RAY DIFFRACTIONTIGHT THERMAL49.680.71
LS refinement shellResolution: 3.26→3.344 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 58 -
Rwork0.408 1032 -
obs--96.04 %
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)
10.32910.7317-0.32293.3348-0.14313.09140.0336-0.04650.2874-0.1332-0.0524-0.4537-1.0276-0.22110.01870.58020.1001-0.02780.2415-0.04531.18320.48433.484-0.939
22.5172-2.18562.3158.58390.93083.6069-0.22650.04841.1433-0.57280.0051-2.1432-0.81440.07950.22150.7811-0.18170.2960.08270.08091.63318.99436.632.384
31.42950.3782-1.43013.79781.18692.59330.1172-0.42190.72030.90670.36750.227-0.14680.1618-0.48470.83370.3188-0.14870.6958-0.3920.4654-7.40125.62420.25
43.0871-5.1854-0.783811.8569-0.75122.3724-0.1669-0.83111.20391.71360.8069-1.038-0.95160.1852-0.641.24410.14750.06640.9856-0.87951.0429-3.80823.83629.041
52.1181-0.22441.95941.4078-1.07362.73870.07470.33540.7384-0.7942-0.31080.32790.04140.28490.23611.16290.37250.04350.68470.26770.5194-8.59924.43-21.226
64.0619-4.5232.31137.3248-2.66191.43160.19741.23970.5292-0.7531-0.56180.9693-0.02440.54630.36441.29940.097-0.15760.88530.61481.3598-0.98226.685-26.73
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 146
2X-RAY DIFFRACTION2A147 - 195
3X-RAY DIFFRACTION3B1 - 146
4X-RAY DIFFRACTION4B147 - 195
5X-RAY DIFFRACTION5C1 - 146
6X-RAY DIFFRACTION6C147 - 195

+
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