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- PDB-7atk: Crystal structure of UipA in complex with Uranium -

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Basic information

Entry
Database: PDB / ID: 7atk
TitleCrystal structure of UipA in complex with Uranium
ComponentsUipA
KeywordsMETAL BINDING PROTEIN / Membrane protein / metal binding
Function / homologymembrane / URANIUM ATOM / PepSY domain-containing protein
Function and homology information
Biological speciesMicrobacterium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.855 Å
AuthorsBremond, N. / Gallois, N. / Legrand, P. / Chapon, V. / Arnoux, P.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS)Needs-Resources Program France
CitationJournal: Isme J / Year: 2022
Title: Discovery and characterization of UipA, a uranium- and iron-binding PepSY protein involved in uranium tolerance by soil bacteria.
Authors: Gallois, N. / Alpha-Bazin, B. / Bremond, N. / Ortet, P. / Barakat, M. / Piette, L. / Mohamad Ali, A. / Lemaire, D. / Legrand, P. / Theodorakopoulos, N. / Floriani, M. / Fevrier, L. / Den ...Authors: Gallois, N. / Alpha-Bazin, B. / Bremond, N. / Ortet, P. / Barakat, M. / Piette, L. / Mohamad Ali, A. / Lemaire, D. / Legrand, P. / Theodorakopoulos, N. / Floriani, M. / Fevrier, L. / Den Auwer, C. / Arnoux, P. / Berthomieu, C. / Armengaud, J. / Chapon, V.
History
DepositionOct 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: UipA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,66910
Polymers21,3891
Non-polymers1,2799
Water00
1
AAA: UipA
hetero molecules

AAA: UipA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,33720
Polymers42,7792
Non-polymers2,55818
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8130 Å2
ΔGint-311 kcal/mol
Surface area13130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.160, 95.160, 52.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11AAA-304-

ZN

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Components

#1: Protein UipA


Mass: 21389.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microbacterium sp. (bacteria) / Gene: CVS53_03692 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3Q9JIL7
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-U1 / URANIUM ATOM


Mass: 238.029 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: U / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.78 Å3/Da / Density % sol: 55.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: MES pH6 100mM, PEG6K 22%, Formamide 6%, ZnCl2 5-15mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.3051 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3051 Å / Relative weight: 1
ReflectionResolution: 2.85→47 Å / Num. obs: 10684 / % possible obs: 99.6 % / Redundancy: 14 % / CC1/2: 0.99 / Net I/σ(I): 12.2
Reflection shellResolution: 2.85→3.03 Å / Num. unique obs: 1700 / CC1/2: 0.76

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ATH

7ath


Resolution: 2.855→47 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.922 / SU B: 13.73 / SU ML: 0.253 / Cross valid method: FREE R-VALUE / ESU R: 0.445 / ESU R Free: 0.282
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.234 298 5.003 %
Rwork0.207 5658 -
all0.208 --
obs-5956 99.649 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 80.529 Å2
Baniso -1Baniso -2Baniso -3
1--2.794 Å20 Å20 Å2
2---2.794 Å20 Å2
3---5.588 Å2
Refinement stepCycle: LAST / Resolution: 2.855→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms962 0 9 0 971
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.013967
X-RAY DIFFRACTIONr_bond_other_d0.0010.017883
X-RAY DIFFRACTIONr_angle_refined_deg1.7821.6291322
X-RAY DIFFRACTIONr_angle_other_deg1.2861.5882038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0825134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg50.07824.78346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.4715141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.546155
X-RAY DIFFRACTIONr_chiral_restr0.0760.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021130
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02177
X-RAY DIFFRACTIONr_nbd_refined0.230.2169
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.2758
X-RAY DIFFRACTIONr_nbtor_refined0.1520.2449
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2528
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2230.217
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0260.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1420.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1920.213
X-RAY DIFFRACTIONr_nbd_other0.1790.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3340.27
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1250.21
X-RAY DIFFRACTIONr_mcbond_it7.1218.393542
X-RAY DIFFRACTIONr_mcbond_other7.0698.396541
X-RAY DIFFRACTIONr_mcangle_it10.58512.565674
X-RAY DIFFRACTIONr_mcangle_other10.59812.567675
X-RAY DIFFRACTIONr_scbond_it9.5529.095425
X-RAY DIFFRACTIONr_scbond_other9.5469.098426
X-RAY DIFFRACTIONr_scangle_it14.27313.296648
X-RAY DIFFRACTIONr_scangle_other14.26213.3649
X-RAY DIFFRACTIONr_lrange_it16.55599.73942
X-RAY DIFFRACTIONr_lrange_other16.54799.781943
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.855-2.9290.331200.3383910.3384310.7290.71895.35960.316
2.929-3.0090.322210.3193960.3194170.7940.7761000.298
3.009-3.0950.296210.2933880.2934090.8490.8271000.269
3.095-3.190.28190.2673770.2683960.8480.8761000.247
3.19-3.2940.223200.2193730.223930.9220.9021000.199
3.294-3.4090.268180.2023370.2053550.8680.9251000.183
3.409-3.5370.375180.2033530.2113710.8770.9321000.186
3.537-3.6810.168170.1913170.193340.9360.9371000.179
3.681-3.8440.222170.1773220.1793390.9310.9461000.164
3.844-4.030.254160.1653110.173270.9430.9561000.158
4.03-4.2460.125150.1552800.1532950.9750.9621000.152
4.246-4.5020.167150.1252870.1273020.9720.9731000.124
4.502-4.8090.185140.142610.1422750.9680.9711000.143
4.809-5.190.295130.1672510.1742640.9480.9561000.173
5.19-5.6790.177120.22240.1992360.9710.9421000.199
5.679-6.3380.3110.2042120.2082230.8910.9431000.206
6.338-7.2970.269100.2081880.2111980.9170.9251000.226
7.297-8.8850.20990.1951640.1961730.9180.9321000.231
8.885-12.3510.23670.2331350.2331420.9160.9241000.259
12.351-47.580.28350.414910.404960.9150.861000.486

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