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- PDB-6hfb: Outward-facing conformation of a multidrug resistance MATE family... -

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Basic information

Entry
Database: PDB / ID: 6hfb
TitleOutward-facing conformation of a multidrug resistance MATE family transporter of the MOP superfamily.
ComponentsUncharacterized protein
KeywordsMEMBRANE PROTEIN / TRANSPORTER
Function / homology: / Multi antimicrobial extrusion protein / MatE / antiporter activity / xenobiotic transmembrane transporter activity / plasma membrane / : / MATE family efflux transporter
Function and homology information
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.495 Å
AuthorsNonaka, T. / Zakrzewska, S. / Safarian, S. / Michel, H.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation Germany
Max Planck Society Germany
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Inward-facing conformation of a multidrug resistance MATE family transporter.
Authors: Zakrzewska, S. / Mehdipour, A.R. / Malviya, V.N. / Nonaka, T. / Koepke, J. / Muenke, C. / Hausner, W. / Hummer, G. / Safarian, S. / Michel, H.
History
DepositionAug 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,62016
Polymers209,0264
Non-polymers1,59512
Water0
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7885
Polymers52,2561
Non-polymers5324
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5223
Polymers52,2561
Non-polymers2662
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6554
Polymers52,2561
Non-polymers3993
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6554
Polymers52,2561
Non-polymers3993
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)219.752, 94.246, 138.785
Angle α, β, γ (deg.)90.00, 126.48, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-502-

CS

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Components

#1: Protein
Uncharacterized protein


Mass: 52256.383 Da / Num. of mol.: 4 / Mutation: A298T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Gene: PF0708 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U2X0
#2: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cs

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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: 2.73 Å3/Da / Density % sol: 54.93 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG 2000 MME, 0.1 M ADA, pH 6.5, 0.15% octyl-beta-D-selenoglucoside; crystal soaking in 1 M CsCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.2 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 3.495→47.13 Å / Num. obs: 54531 / % possible obs: 99.3 % / Redundancy: 3.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.054 / Rrim(I) all: 0.106 / Net I/av σ(I): 15.1 / Net I/σ(I): 7.3
Reflection shellResolution: 3.495→3.62 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 5 / Num. unique obs: 2738 / CC1/2: 0.908 / Rpim(I) all: 0.188 / Rrim(I) all: 0.37 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MLB

4mlb


Resolution: 3.495→19.999 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2392 2711 5 %
Rwork0.189 --
obs0.1915 54264 96.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.495→19.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13594 0 12 0 13606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213871
X-RAY DIFFRACTIONf_angle_d0.41518813
X-RAY DIFFRACTIONf_dihedral_angle_d10.4178159
X-RAY DIFFRACTIONf_chiral_restr0.0352308
X-RAY DIFFRACTIONf_plane_restr0.0032297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4947-3.55790.3133960.26772330X-RAY DIFFRACTION82
3.5579-3.62590.31941530.26712723X-RAY DIFFRACTION97
3.6259-3.69950.36011430.2492689X-RAY DIFFRACTION97
3.6995-3.77940.31731590.22192808X-RAY DIFFRACTION98
3.7794-3.86670.26661460.20762745X-RAY DIFFRACTION98
3.8667-3.96270.3481410.20662788X-RAY DIFFRACTION98
3.9627-4.0690.22551400.18882709X-RAY DIFFRACTION97
4.069-4.18770.21831460.17942758X-RAY DIFFRACTION98
4.1877-4.32150.23781410.1732750X-RAY DIFFRACTION97
4.3215-4.47430.20321390.16872687X-RAY DIFFRACTION96
4.4743-4.65130.20931530.16562723X-RAY DIFFRACTION97
4.6513-4.86010.20831410.16172732X-RAY DIFFRACTION98
4.8601-5.11230.20971520.17312775X-RAY DIFFRACTION98
5.1123-5.42660.27231550.19812805X-RAY DIFFRACTION98
5.4266-5.83590.25551600.21672706X-RAY DIFFRACTION98
5.8359-6.40560.28151510.21542693X-RAY DIFFRACTION96
6.4056-7.29290.24561410.18682758X-RAY DIFFRACTION96
7.2929-9.04450.15291360.13942708X-RAY DIFFRACTION97
9.0445-19.99920.20691180.18192666X-RAY DIFFRACTION94

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