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- PDB-3ux4: Crystal structure of the urea channel from the human gastric path... -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water00
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

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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

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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: 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

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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

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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

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