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- PDB-8tgy: Crystal structure of Gdx-Clo from Small Multidrug Resistance fami... -

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Basic information

Entry
Database: PDB / ID: 8tgy
TitleCrystal structure of Gdx-Clo from Small Multidrug Resistance family of transporters in complex with guanylurea
Components
  • L10 Monobody
  • Multidrug resistance protein, SMR familyMultiple drug resistance
KeywordsTRANSPORT PROTEIN / SMR / Gdx-Clo / antiporter / gunaylurea
Function / homologySmall drug/metabolite transporter protein family / Small multidrug resistance protein / Small Multidrug Resistance protein / transmembrane transporter activity / plasma membrane / N-(diaminomethylidene)urea / Multidrug resistance protein, SMR family
Function and homology information
Biological speciesClostridia bacterium (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsLucero, R.M. / Stockbridge, R.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35- GM128768 United States
CitationJournal: Biorxiv / Year: 2023
Title: Transport of metformin metabolites by guanidinium exporters of the Small Multidrug Resistance family.
Authors: Lucero, R.M. / Demirer, K. / Yeh, T.J. / Stockbridge, R.B.
History
DepositionJul 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Multidrug resistance protein, SMR family
E: Multidrug resistance protein, SMR family
G: Multidrug resistance protein, SMR family
B: Multidrug resistance protein, SMR family
C: L10 Monobody
D: L10 Monobody
F: L10 Monobody
H: L10 Monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,53917
Polymers85,0958
Non-polymers2,4449
Water48627
1
A: Multidrug resistance protein, SMR family
E: Multidrug resistance protein, SMR family
C: L10 Monobody
F: L10 Monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8209
Polymers42,5484
Non-polymers1,2735
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Multidrug resistance protein, SMR family
B: Multidrug resistance protein, SMR family
D: L10 Monobody
H: L10 Monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7188
Polymers42,5484
Non-polymers1,1714
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.914, 74.371, 107.212
Angle α, β, γ (deg.)86.77, 90.01, 70.26
Int Tables number1
Space group name H-MP1

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Components

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Protein / Antibody / Sugars , 3 types, 10 molecules AEGBCDFH

#1: Protein
Multidrug resistance protein, SMR family / Multiple drug resistance


Mass: 11341.865 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridia bacterium (bacteria) / Gene: HMPREF1982_00479 / Production host: Escherichia coli (E. coli) / References: UniProt: U2EQ00
#2: Antibody
L10 Monobody


Mass: 9931.934 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 3 types, 34 molecules

#3: Chemical ChemComp-9U1 / N-(diaminomethylidene)urea


Mass: 102.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6N4O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.39 Å3/Da / Density % sol: 72.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES pH 7.0, 0.1 M calcium acetate, 31% PEG600

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.18→107 Å / Num. obs: 29224 / % possible obs: 81.1 % / Redundancy: 3.3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.069 / Rrim(I) all: 0.122 / Net I/σ(I): 18.1
Reflection shellResolution: 2.18→2.55 Å / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1577 / CC1/2: 0.739 / Rpim(I) all: 0.356 / Rrim(I) all: 0.698 / % possible all: 69.8

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
DIALSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→35.66 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 44.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3086 1360 4.67 %
Rwork0.2801 --
obs0.2815 27820 81.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.18→35.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5873 0 158 27 6058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036185
X-RAY DIFFRACTIONf_angle_d0.598451
X-RAY DIFFRACTIONf_dihedral_angle_d11.8782115
X-RAY DIFFRACTIONf_chiral_restr0.0421030
X-RAY DIFFRACTIONf_plane_restr0.004966
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.260.470260.3651105X-RAY DIFFRACTION1
2.26-2.350.2746150.388256X-RAY DIFFRACTION4
2.35-2.460.4352190.3477520X-RAY DIFFRACTION7
2.46-2.590.4104430.3572851X-RAY DIFFRACTION12
2.59-2.750.4143510.33831180X-RAY DIFFRACTION16
2.75-2.960.35911120.34482340X-RAY DIFFRACTION33
2.97-3.260.33122080.32164275X-RAY DIFFRACTION60
3.26-3.730.34582710.28786438X-RAY DIFFRACTION89
3.74-4.70.31943490.26216175X-RAY DIFFRACTION87
4.7-35.660.25362860.26215644X-RAY DIFFRACTION79

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