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- PDB-3m6e: F80A mutant of the Urea Transporter from Desulfovibrio Vulgaris -

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Basic information

Entry
Database: PDB / ID: 3m6e
TitleF80A mutant of the Urea Transporter from Desulfovibrio Vulgaris
ComponentsPutative urea transporter
KeywordsTRANSPORT PROTEIN / Membrane protein / channel / urea transport / 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: 2.65 Å
AuthorsLevin, E.J. / Zhou, M. / New York Consortium on Membrane Protein Structure (NYCOMPS)
CitationJournal: To be Published
Title: F80A mutant of the Urea Transporter from Desulfovibrio Vulgaris
Authors: Levin, E.J. / Zhou, M.
History
DepositionMar 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: 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 1.3Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...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
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative urea transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,71110
Polymers35,9381
Non-polymers1,7739
Water34219
1
A: Putative urea transporter
hetero molecules

A: Putative urea transporter
hetero molecules

A: Putative urea transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,13330
Polymers107,8153
Non-polymers5,31827
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area13920 Å2
ΔGint-273 kcal/mol
Surface area35470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.558, 110.558, 84.523
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 Putative urea transporter


Mass: 35938.391 Da / Num. of mol.: 1 / Mutation: F80A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Strain: Hildenborough / Gene: DVU_1160 / Plasmid: pET SUMO / 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.: 19 / 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: 4.16 Å3/Da / Density % sol: 70.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 26% PEG 1500, 100 mM Na Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1.2135 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 19, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2135 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 16528 / % possible obs: 96.4 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.113 / Χ2: 1.186 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.65-2.73.30.9538411.45398.4
2.7-2.743.80.8028321.60698
2.74-2.84.30.7138171.29798
2.8-2.854.90.7538401.37998.6
2.85-2.925.40.6718401.27896.9
2.92-2.985.80.5738481.54598.4
2.98-3.066.10.518221.18398
3.06-3.146.30.4328311.10796.9
3.14-3.236.50.3518351.07697.3
3.23-3.346.40.2888201.11797.6
3.34-3.466.40.2088320.97697.2
3.46-3.66.40.1738331.26697.2
3.6-3.765.90.3428252.08796.5
3.76-3.966.40.1248331.02496.2
3.96-4.216.50.0898120.94395.9
4.21-4.536.50.0798150.96696
4.53-4.996.40.0728261.0195.1
4.99-5.716.30.0628170.91595.6
5.71-7.196.50.068300.98994.7
7.19-5060.0667791.0886.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å47.87 Å
Translation3.5 Å47.87 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3K3F

3k3f


Resolution: 2.65→47.89 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.248 / WRfactor Rwork: 0.212 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.838 / SU B: 17.689 / SU ML: 0.187 / SU R Cruickshank DPI: 0.36 / SU Rfree: 0.249 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.356 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.224 824 5 %RANDOM
Rwork0.194 ---
obs0.195 16438 95.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 135.15 Å2 / Biso mean: 78.352 Å2 / Biso min: 54.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20.33 Å20 Å2
2--0.65 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 2.65→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2484 0 9 19 2512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222544
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.973465
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8765331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.26122.85784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.18615385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.259159
X-RAY DIFFRACTIONr_chiral_restr0.0980.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021876
X-RAY DIFFRACTIONr_nbd_refined0.2260.21268
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21825
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.288
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.25
X-RAY DIFFRACTIONr_mcbond_it0.5761.51683
X-RAY DIFFRACTIONr_mcangle_it0.98522630
X-RAY DIFFRACTIONr_scbond_it1.5233987
X-RAY DIFFRACTIONr_scangle_it2.3254.5835
LS refinement shellResolution: 2.653→2.722 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 59 -
Rwork0.241 1170 -
all-1229 -
obs-1170 96.54 %
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)
11.41180.8984-0.32862.30381.58321.93120.02470.3228-0.77110.0793-0.13260.55530.4755-0.15450.10790.41540.04390.1749-0.0764-0.16210.3318-55.147-1.1262-7.273
22.6770.1610.81022.72760.31091.0361-0.09180.0735-0.5548-0.0294-0.18680.210.4298-0.21850.2787-0.0225-0.04580.105-0.2-0.0834-0.0884-61.239714.23480.7316
31.9814-0.0275-0.84082.17840.62022.9712-0.1988-0.2174-0.87410.4476-0.1369-0.65120.84970.54630.33570.18170.18030.1038-0.00660.18190.2492-40.53137.46647.421
41.75560.273-0.33192.4503-0.45821.8397-0.14840.0267-0.3962-0.0786-0.1608-0.54210.37470.46870.3093-0.13190.0840.0837-0.09990.0985-0.0787-40.848619.02362.0346
51.44292.66140.682113.35832.70283.3711-0.41330.9213-0.5547-1.72910.180.10760.24770.15430.23330.3370.06370.37590.3457-0.04780.2428-39.282815.5402-18.6367
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 52
2X-RAY DIFFRACTION2A53 - 158
3X-RAY DIFFRACTION3A159 - 215
4X-RAY DIFFRACTION4A216 - 309
5X-RAY DIFFRACTION5A310 - 334

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