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- PDB-3me1: Crystal Structure of the Desulfovibro vulgaris Urea Transporter i... -

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Basic information

Entry
Database: PDB / ID: 3me1
TitleCrystal Structure of the Desulfovibro vulgaris Urea Transporter in the P3(1) Space Group at 3.86
ComponentsUrea transporter
KeywordsTRANSPORT PROTEIN / Membrane protein / channel / Structural Genomics / PSI-2 / Protein Structure Initiative / New York Consortium on Membrane Protein Structure / NYCOMPS
Function / homology
Function and homology information


urea binding / urea channel activity / urea transmembrane transport / protein homotrimerization / identical protein binding / plasma membrane
Similarity search - Function
Urea transporter / Urea transporter / Ammonium transporter fold / Ammonium transporter AmtB like domains / Ammonium/urea transporter / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Urea transporter DVU1160
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.862 Å
AuthorsLevin, E.J. / Zhou, M. / New York Consortium on Membrane Protein Structure (NYCOMPS)
CitationJournal: To be Published
Title: Crystal Structure of the Desulfovibro vulgaris Urea Transporter in the P3(1) Space Group at 3.86 .
Authors: Levin, E.J. / Zhou, M.
History
DepositionMar 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Urea transporter
B: Urea transporter
C: Urea transporter


Theoretical massNumber of molelcules
Total (without water)106,4853
Polymers106,4853
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.197, 103.197, 141.498
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1PROPROILEILEchain AAA10 - 3348 - 332
2LYSLYSILEILEchain BBB8 - 3346 - 332
3PROPROVALVALchain C and not resid 334CC10 - 258 - 23

NCS oper:
IDCodeMatrixVector
1given(-0.474252, 0.869131, -0.140345), (-0.84776, -0.493832, -0.193475), (-0.237461, 0.027223, 0.971015)25.908501, 103.467003, 9.30734
2given(-0.494056, -0.840801, -0.221273), (0.857896, -0.512767, 0.032931), (-0.14115, -0.17356, 0.974656)102.459, 29.799101, 13.9139
DetailsThe biological assembly is the asymmetric unit.

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Components

#1: Protein Urea transporter


Mass: 35494.910 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Strain: Hildenborough / Gene: DVU_1160 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q72CX3

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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: 4.09 Å3/Da / Density % sol: 69.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.25
Details: 22% PEG 1500, 100 mM Na Cacodylate, pH 6.25, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 3, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.85→50 Å / Num. obs: 15450 / % possible obs: 97.7 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.067 / Χ2: 1.096 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.85-3.9270.5826241.107181.4
3.92-3.997.50.7427261.182188.5
3.99-4.068.30.527511.159195.5
4.06-4.159.10.4977631.143197.6
4.15-4.249.70.397851.1731100
4.24-4.3410.40.3147681.19199.9
4.34-4.4410.90.3198351.171100
4.44-4.5611.30.2157801.1841100
4.56-4.711.50.187901.1651100
4.7-4.8511.60.1647911.1331100
4.85-5.0211.60.1397761.091100
5.02-5.2211.70.1487981.0881100
5.22-5.4611.70.1358041.127199.9
5.46-5.7511.60.1137851.1191100
5.75-6.1111.60.1157841.0611100
6.11-6.5811.60.1047761.0051100
6.58-7.2411.60.0817990.9911100
7.24-8.2811.50.0547941.002199.9
8.28-10.4211.20.0388021.0431100
10.42-5010.90.0327190.87190.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.5 Å48.48 Å
Translation4.5 Å48.48 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.862→34.813 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.5974 / SU ML: 0.82 / σ(F): 1.96 / Phase error: 44.57 / Stereochemistry target values: ML
Details: POLYALANINE MODEL INTENDED FOR ANALYSIS OF CRYSTAL PACKING. FOR THE HIGH RESOLUTION STRUCTURE SEE 3K3F
RfactorNum. reflection% reflection
Rfree0.3866 773 5.03 %
Rwork0.3206 14604 -
obs0.3239 15377 97.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 215.535 Å2 / ksol: 0.139 e/Å3
Displacement parametersBiso max: 577.67 Å2 / Biso mean: 251.2757 Å2 / Biso min: 49.23 Å2
Baniso -1Baniso -2Baniso -3
1-18.8697 Å20 Å2-0 Å2
2--18.8697 Å20 Å2
3----41.0777 Å2
Refinement stepCycle: LAST / Resolution: 3.862→34.813 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4673 0 0 0 4673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044665
X-RAY DIFFRACTIONf_angle_d0.9456454
X-RAY DIFFRACTIONf_chiral_restr0.049849
X-RAY DIFFRACTIONf_plane_restr0.002948
X-RAY DIFFRACTIONf_dihedral_angle_d20.1272844
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1569X-RAY DIFFRACTIONPOSITIONAL0.024
12B1569X-RAY DIFFRACTIONPOSITIONAL0.024
13C1526X-RAY DIFFRACTIONPOSITIONAL0.026
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.862-4.10370.3742960.36462247234389
4.1037-4.41990.38221340.34462470260499
4.4199-4.86370.38771380.354324902628100
4.8637-5.5650.50381370.386124882625100
5.565-7.00190.50611410.393124992640100
7.0019-34.81450.30621270.26122410253797
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)
12.70792.93722.73593.09532.92252.76960.87991.4231.8999-0.83212.30282.76111.454-2.4775-0.4599-0.2205-4.2214-0.48533.49330.30842.191323.583222.0829-8.9615
22.7246-0.3228-0.90594.46681.78592.04012.1564-0.5096-0.87530.9525-1.40062.47920.3322-4.59250.5286-1.29570.04480.80813.38520.71382.041821.417331.998-1.979
34.21621.2376-0.74983.4126-0.88651.7737-0.1602-2.854-1.4180.7887-0.90080.5751-0.75660.45040.00490.14530.60750.10761.83720.51381.323833.561138.7062-4.9885
40.20620.25711.01870.10940.83075.23191.0694-0.83890.33252.06180.30871.38872.6178-5.3115-2.6608-1.4637-1.73552.0551.13362.32441.820232.697622.649610.237
52.43992.0628-2.62892.8626-2.18632.8428-0.36090.60090.1832-1.21620.1684-2.20160.9562-2.99010.02341.8058-0.37490.59750.81710.05690.913742.335619.23072.5195
66.27591.40392.4542.867-0.47051.1115-0.191-0.5717-0.4338-0.29091.13450.15120.8815-0.574-0.20490.5442-0.5919-0.1052.05360.16280.456245.004227.0615-4.8649
74.18051.92233.64881.17661.76793.73051.2825-0.03452.1151-1.14551.4601-2.19860.17470.5601-3.18930.72540.02420.64041.9654-0.69842.460574.880836.9828-1.4007
84.76582.97154.1682.0424-0.60988.21530.0526-1.1989-2.1323-4.56652.6608-1.9288-0.03281.31630.66850.8508-0.12880.66380.9747-0.2961.109665.5331.22042.9629
98.30791.70693.62297.0688-1.3984.18480.1063-2.93650.51521.572-0.6719-0.6772-2.3243-1.84460.92420.70950.1098-0.03970.6892-0.36330.413754.095637.25346.896
107.13554.3028-5.71133.4721-1.76161.93351.5929-0.76593.357-0.20242.49190.0378-3.52361.86750.39711.6803-1.42060.13581.484-0.51821.226368.256154.0078.5996
112.59-1.2351-1.40055.59372.97771.785-0.0668-2.1001-0.608-1.51460.0693-1.1357-0.74610.39610.66461.73591.02160.28451.0478-0.06910.320654.226150.46659.1233
126.0759-2.81242.5962.6009-2.86723.1567-2.5235-3.27350.4066-0.32693.3619-0.714-4.45550.0114-0.94932.2284-1.19330.78832.7252-0.30310.870563.364755.7054-12.5029
131.3324-1.299-0.98361.27280.99740.78641.0685-0.5823-0.1748-0.80391.58380.08020.0021-0.18050.63726.31223.34050.47990.61421.82863.107435.480874.3574-4.6958
146.10431.8093-2.95060.7444-0.85222.2-2.3361-0.41854.06670.05763.57391.973-2.78520.0497-1.70835.05310.7633-0.10050.63360.04782.947243.456969.7802-0.5619
152.67570.3174-2.37720.90261.07693.72451.3287-1.60311.83430.65710.98210.732-1.9166-0.45520.61742.84521.07621.05571.5252-0.59441.368643.99258.31067.197
160.93341.225-1.17712.0254-1.48521.4968-0.895-1.88921.411-1.70031.66420.8151.00810.6155-0.23443.10351.85230.31442.8374-1.09691.784124.014868.18926.6053
171.16841.2720.68511.9353-0.84444.2373-0.6109-2.8165-1.63850.48591.85651.35950.4687-0.1455-0.38321.49743.06421.24822.2636-0.26923.493222.418559.30641.4813
182.8072-1.7541.69225.051-1.59811.6363-0.6253-0.5283-0.20711.23670.94070.8947-1.8295-2.2855-0.31843.26011.72610.23851.66130.47860.926528.442353.0774-5.9343
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid -1:41)A-1 - 41
2X-RAY DIFFRACTION2(chain A and resid 42:107)A42 - 107
3X-RAY DIFFRACTION3(chain A and resid 108:142)A108 - 142
4X-RAY DIFFRACTION4(chain A and resid 143:209)A143 - 209
5X-RAY DIFFRACTION5(chain A and resid 210:260)A210 - 260
6X-RAY DIFFRACTION6(chain A and resid 261:334)A261 - 334
7X-RAY DIFFRACTION7(chain B and resid 1:43)B1 - 43
8X-RAY DIFFRACTION8(chain B and resid 44:101)B44 - 101
9X-RAY DIFFRACTION9(chain B and resid 102:169)B102 - 169
10X-RAY DIFFRACTION10(chain B and resid 170:266)B170 - 266
11X-RAY DIFFRACTION11(chain B and resid 267:301)B267 - 301
12X-RAY DIFFRACTION12(chain B and resid 302:334)B302 - 334
13X-RAY DIFFRACTION13(chain C and resid 0:43)C0 - 43
14X-RAY DIFFRACTION14(chain C and resid 44:94)C44 - 94
15X-RAY DIFFRACTION15(chain C and resid 95:165)C95 - 165
16X-RAY DIFFRACTION16(chain C and resid 168:204)C168 - 204
17X-RAY DIFFRACTION17(chain C and resid 205:258)C205 - 258
18X-RAY DIFFRACTION18(chain C and resid 259:334)C259 - 334

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