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- PDB-3k3g: Crystal Structure of the Urea Transporter from Desulfovibrio Vulg... -

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Basic information

Entry
Database: PDB / ID: 3k3g
TitleCrystal Structure of the Urea Transporter from Desulfovibrio Vulgaris Bound to 1,3-dimethylurea
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
: / 1,3-dimethylurea / Urea transporter DVU1160
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 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: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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)37,96312
Polymers36,0141
Non-polymers1,94911
Water50428
1
A: Urea transporter
hetero molecules

A: Urea transporter
hetero molecules

A: Urea transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,89036
Polymers108,0433
Non-polymers5,84733
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 area10090 Å2
ΔGint-110 kcal/mol
Surface area36080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.106, 110.106, 84.872
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: Chemical ChemComp-MMU / 1,3-dimethylurea


Mass: 88.108 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8N2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 1

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Sample preparation

CrystalDensity Matthews: 4.14 Å3/Da / Density % sol: 70.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 23% PEG 1500, 100 mM Na Cacodylate, 10 mM N,N'-dimethylurea, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 5, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 22979 / % possible obs: 99.5 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.091 / Χ2: 0.712 / Net I/σ(I): 8.5
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.915 / Num. unique all: 1138 / Χ2: 0.427 / % possible all: 97.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4 Å26.45 Å
Translation4 Å26.45 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K3F

3k3f


Resolution: 2.4→27.47 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.222 / WRfactor Rwork: 0.194 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.872 / SU B: 11.143 / SU ML: 0.133 / SU R Cruickshank DPI: 0.216 / SU Rfree: 0.183 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1166 5.1 %RANDOM
Rwork0.186 ---
all0.187 22964 --
obs0.187 22964 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.09 Å2 / Biso mean: 44.871 Å2 / Biso min: 30.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20.22 Å20 Å2
2--0.45 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.4→27.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2481 0 21 28 2530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222554
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.9723476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.495329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.84622.82485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73715386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.68159
X-RAY DIFFRACTIONr_chiral_restr0.1040.2414
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021891
X-RAY DIFFRACTIONr_nbd_refined0.2060.21316
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21807
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.288
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.25
X-RAY DIFFRACTIONr_mcbond_it0.5591.51681
X-RAY DIFFRACTIONr_mcangle_it0.98522621
X-RAY DIFFRACTIONr_scbond_it1.46831005
X-RAY DIFFRACTIONr_scangle_it2.1014.5855
LS refinement shellResolution: 2.4→2.459 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 77 -
Rwork0.242 1573 -
all-1650 -
obs--98.33 %
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)
14.8342-1.69299.0627.9641-13.012430.1202-0.6349-0.30580.02390.2416-0.7059-0.760.2275-0.02171.34080.42790.06810.07090.03370.35710.317160.67565.3778-18.4165
22.19770.1097-0.19391.998-0.25461.5486-0.15330.02430.60720.0216-0.2017-0.0641-0.44420.030.3550.2863-0.0059-0.15420.06280.03150.239956.3248-11.12292.1456
31.63660.17480.00481.5598-0.08481.6575-0.14110.09790.4876-0.0226-0.17410.4281-0.3122-0.32620.31520.19420.0919-0.14270.1491-0.08980.265440.8581-15.23461.3617
49.79482.1701-2.328619.0035-2.37648.0071-0.16691.03770.7335-2.53930.0064-0.5474-0.35370.00660.16050.28690.1595-0.420.23860.116-0.050239.49-12.7689-19.0106
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 15
2X-RAY DIFFRACTION2A16 - 181
3X-RAY DIFFRACTION3A182 - 312
4X-RAY DIFFRACTION4A313 - 334

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