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- PDB-4hun: MATE transporter NorM-NG in complex with R6G and monobody -

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Basic information

Entry
Database: PDB / ID: 4hun
TitleMATE transporter NorM-NG in complex with R6G and monobody
Components
  • Multidrug efflux protein
  • protein B
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


cell-substrate junction assembly / proteoglycan binding / extracellular matrix structural constituent / cell-matrix adhesion / integrin binding
Similarity search - Function
: / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
RHODAMINE 6G / : / Protein B
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 3.59 Å
AuthorsLu, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structures of a Na+-coupled, substrate-bound MATE multidrug transporter.
Authors: Lu, M. / Symersky, J. / Radchenko, M. / Koide, A. / Guo, Y. / Nie, R. / Koide, S.
History
DepositionNov 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Apr 28, 2021Group: Advisory / Database references / Derived calculations
Category: database_PDB_caveat / struct_ref_seq_dif / struct_site
Item: _struct_ref_seq_dif.details / _struct_site.pdbx_auth_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 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multidrug efflux protein
B: protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0783
Polymers60,6352
Non-polymers4441
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Multidrug efflux protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1612
Polymers49,7181
Non-polymers4441
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: protein B


Theoretical massNumber of molelcules
Total (without water)10,9171
Polymers10,9171
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.234, 117.234, 226.218
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Multidrug efflux protein


Mass: 49717.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: NGTW08_0430 / Production host: Escherichia coli (E. coli) / References: UniProt: E8SM44
#2: Protein protein B


Mass: 10916.989 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: M1E1G6*PLUS
#3: Chemical ChemComp-RHQ / RHODAMINE 6G


Mass: 443.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H31N2O3

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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: 7.4 Å3/Da / Density % sol: 83.38 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 8 / Details: PEG, pH 8, VAPOR DIFFUSION, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Jan 1, 2010
RadiationMonochromator: 1 A / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.59→60 Å / Num. all: 22000 / Num. obs: 21652 / % possible obs: 99.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 3.59→20 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.907 / SU B: 99.088 / SU ML: 0.579 / Cross valid method: THROUGHOUT / ESU R: 1.22 / ESU R Free: 0.544
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.32747 1104 5.1 %RANDOM
Rwork0.30593 ---
obs0.30704 20561 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 178.253 Å2
Baniso -1Baniso -2Baniso -3
1-6.96 Å23.48 Å20 Å2
2--6.96 Å20 Å2
3----10.44 Å2
Refinement stepCycle: LAST / Resolution: 3.59→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4215 0 33 0 4248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.024370
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3281.9625953
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.575548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34721.788151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg27.22115658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4131520
X-RAY DIFFRACTIONr_chiral_restr0.1790.2670
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213259
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.588→3.678 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 68 -
Rwork0.44 1317 -
obs--98.79 %
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)
11.86190.49171.99110.3180.99083.3990.05050.4905-0.2409-0.0307-0.01290.0161-0.19490.3828-0.03760.2428-0.0757-0.00130.795-0.01150.48517.7106-48.751726.8693
20.88050.9648-1.82193.0525-1.49413.943-0.0684-0.2513-0.05140.04250.0115-0.15660.12790.41370.0570.23380.2789-0.02640.8427-0.030.3962-31.7732-59.52828.6106
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 463
2X-RAY DIFFRACTION2B1 - 91

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