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- PDB-3k3f: Crystal Structure of the Urea Transporter from Desulfovibrio Vulgaris -

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Basic information

Entry
Database: PDB / ID: 3k3f
TitleCrystal Structure of the Urea Transporter from Desulfovibrio Vulgaris
ComponentsUrea transporter
KeywordsTRANSPORT PROTEIN / Membrane protein / channel / urea transport / transporter / 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 / SAD / Resolution: 2.3 Å
AuthorsLevin, E.J. / Zhou, M. / New York Consortium on Membrane Protein Structure (NYCOMPS)
CitationJournal: Nature / Year: 2009
Title: Crystal structure of a bacterial homologue of the kidney urea transporter.
Authors: Levin, E.J. / Quick, M. / Zhou, M.
History
DepositionOct 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Data collection / Refinement description / Category: diffrn / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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: Urea transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,78710
Polymers36,0141
Non-polymers1,7739
Water99155
1
A: Urea transporter
hetero molecules

A: Urea transporter
hetero molecules

A: Urea transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,36230
Polymers108,0433
Non-polymers5,31827
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area10150 Å2
ΔGint-107 kcal/mol
Surface area35890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.131, 110.131, 84.861
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Urea transporter


Mass: 36014.484 Da / Num. of mol.: 1
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
#2: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Au
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.14 Å3/Da / Density % sol: 70.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 23% PEG 1500, 100 mM Na Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A11.01
SYNCHROTRONNSLS X29A21.04
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 2, 2009
Radiation
IDMonochromatorProtocolScattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHx-ray1
2Si(111)SINGLE WAVELENGTHx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.011
21.041
ReflectionRedundancy: 19.5 % / Av σ(I) over netI: 20.12 / Number: 392827 / Rmerge(I) obs: 0.113 / Χ2: 1.12 / D res high: 2.5 Å / D res low: 50 Å / Num. obs: 20107 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.785096.510.091.60619.6
5.386.7810010.091.54819
4.75.3899.910.0891.28719.9
4.274.710010.0921.19720
3.974.2710010.091.22520.2
3.733.9710010.0990.92920.2
3.553.7310010.1080.8920.2
3.393.5510010.1261.16820.2
3.263.3910010.1651.2320
3.153.2610010.2011.29320
3.053.1510010.251.22219.7
2.963.0510010.2991.14719.6
2.892.9610010.3411.07919.6
2.822.8910010.4150.96819.5
2.752.8210010.5170.97219.3
2.692.7510010.6260.9419.2
2.642.6910010.790.9319
2.592.6410010.88618.9
2.542.5910010.85218.6
2.52.5410010.86317.9
ReflectionResolution: 2.3→50 Å / Num. all: 26094 / Num. obs: 25924 / % possible obs: 99.4 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.089 / Χ2: 1.204 / Net I/σ(I): 14.4
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.964 / Num. unique all: 1214 / Χ2: 0.971 / % possible all: 95.2

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-29.50754.276-0.519HG01
2-8.43948.6083.49HG00.77
337.27524.62331.805HG00.6
4-23.34746.66828.572HG00.53
5-9.10351.556.422HG00.45
6-21.72348.33825.625HG00.37

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→38.78 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.213 / WRfactor Rwork: 0.201 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.882 / SU B: 8.86 / SU ML: 0.111 / SU R Cruickshank DPI: 0.192 / SU Rfree: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1293 5 %RANDOM
Rwork0.179 ---
all0.18 25854 --
obs0.18 25854 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.6 Å2 / Biso mean: 48.581 Å2 / Biso min: 30.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20.35 Å20 Å2
2--0.7 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2485 0 9 55 2549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222546
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.973467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.045330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.83622.82485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.0315386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.56159
X-RAY DIFFRACTIONr_chiral_restr0.10.2414
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021879
X-RAY DIFFRACTIONr_nbd_refined0.2090.21336
X-RAY DIFFRACTIONr_nbtor_refined0.310.21816
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2101
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.26
X-RAY DIFFRACTIONr_mcbond_it0.7671.51681
X-RAY DIFFRACTIONr_mcangle_it1.28322624
X-RAY DIFFRACTIONr_scbond_it2.1833995
X-RAY DIFFRACTIONr_scangle_it3.2044.5843
LS refinement shellResolution: 2.3→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 76 -
Rwork0.231 1743 -
all-1819 -
obs--95.69 %
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)
111.5141-1.4531-16.84534.53795.281126.9311-0.19410.2594-1.1528-0.5134-0.4787-0.59191.3145-0.5890.67270.2336-0.04170.1470.42780.15590.424525.749-55.27818.715
21.8923-0.0833-0.09012.4218-0.09941.9133-0.17350.0077-0.3493-0.0112-0.13190.57080.2626-0.40490.3054-0.0729-0.11130.10480.04-0.10330.125237.826-43.373-1.717
31.71530.07440.02922.16630.24662.2-0.1612-0.06460.15470.0682-0.14080.6981-0.1182-0.50130.302-0.12440.0173-0.00780.0719-0.15970.138133.662-27.82-1.093
410.71316.47210.078719.41286.17294.26040.0189-1.2507-0.25281.417-0.53990.72130.2114-0.67270.5210.00940.01520.25240.2129-0.1336-0.05130.91-27.88719.185
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 15
2X-RAY DIFFRACTION2A16 - 181
3X-RAY DIFFRACTION3A182 - 312
4X-RAY DIFFRACTION4A313 - 334

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